Да, со старым приложением та же ошибка. С TLS проблем нет. Ошибка возникает с JCP при вызове:
/* Выработка ключа согласования алисы c SV*/
final KeyAgreement senderKeyAgree =
KeyAgreement.getInstance("GOST3410DH");

Решил пока вернутся к версии 2.0.37538. Устанавливаю JTLS командой:
java -Dfile.encoding=cp866 -cp cpSSL.jar ru.CryptoPro.ssl.JTLSInstall -install -verbose -sslserial xxxxx-xxxxx-xxxxx-xxxxx-xxxxx -sslcompany "company"

Тест java -cp samples.jar ComLine.CheckConfFull выдает, что время лицензии вышло, хотя срок лицензии не ограничен.

Что делать?

ru.CryptoPro.JCP.ControlPane.MainControlPaneConfig:
trusts = C:\rosreestr;
ru.CryptoPro.Crypto.CryptoProvider:
ru.CryptoPro.reprov.RevCheck:
ru.CryptoPro.ssl.ServerSettings:
Enable_revocation_default = false
Enable_CRL_revocation_online_default = false
CRL_location_default =

-SYSTEM PROPERTIES-
java.runtime.name Java(TM) SE Runtime Environment
sun.boot.library.path D:\java\jdk1.7.0_72\jre\bin
java.vm.version 24.72-b04
java.vm.vendor Oracle Corporation
java.vendor.url http://java.oracle.com/
path.separator ;
java.vm.name Java HotSpot(TM) 64-Bit Server VM
file.encoding.pkg sun.io
user.country RU
user.script
sun.java.launcher SUN_STANDARD
sun.os.patch.level Service Pack 1
java.vm.specification.name Java Virtual Machine Specification
user.dir C:\Users\Potapov
java.runtime.version 1.7.0_72-b14
java.awt.graphicsenv sun.awt.Win32GraphicsEnvironment
java.endorsed.dirs D:\java\jdk1.7.0_72\jre\lib\endorsed
os.arch amd64
java.io.tmpdir C:\Users\Potapov\AppData\Local\Temp\
line.separator

java.vm.specification.vendor Oracle Corporation
user.variant
os.name Windows 7
sun.jnu.encoding Cp1251
java.library.path D:\java\jdk1.7.0_72\jre\bin;C:\Windows\Sun\Jav
a\bin;C:\Windows\system32;C:\Windows;C:\Program Files\Crypto Pro\CSP;c:\orant9\b
in;D:\apache-maven-3.1.0\bin;C:\Program Files (x86)\AMD APP\bin\x86_64;C:\Progra
m Files (x86)\AMD APP\bin\x86;C:\Program Files (x86)\Intel\iCLS Client\;C:\Progr
am Files\Intel\iCLS Client\;C:\Windows\system32;C:\Windows;C:\Windows\System32\W
bem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program Files\Intel\Intel(R)
Management Engine Components\DAL;C:\Program Files\Intel\Intel(R) Management Engi
ne Components\IPT;C:\Program Files (x86)\Intel\Intel(R) Management Engine Compon
ents\DAL;C:\Program Files (x86)\Intel\Intel(R) Management Engine Components\IPT;
C:\Program Files (x86)\ATI Technologies\ATI.ACE\Core-Static;C:\Program Files\Mer
curial;C:\Program Files (x86)\sbt\\bin;D:\Java\scala-2.11.0\bin;D:\Java\scala\bi
n;.
java.specification.name Java Platform API Specification
java.class.version 51.0
sun.management.compiler HotSpot 64-Bit Tiered Compilers
os.version 6.1
user.home C:\Users\Potapov
user.timezone
java.awt.printerjob sun.awt.windows.WPrinterJob
file.encoding Cp1251
java.specification.version 1.7
java.class.path .
user.name Potapov
java.vm.specification.version 1.7
sun.java.command ru.CryptoPro.JCP.tools.Check -all
java.home D:\java\jdk1.7.0_72\jre
sun.arch.data.model 64
user.language ru
java.specification.vendor Oracle Corporation
awt.toolkit sun.awt.windows.WToolkit
java.vm.info mixed mode
java.version 1.7.0_72
java.ext.dirs D:\java\jdk1.7.0_72\jre\lib\ext;C:\Windows\Sun
\Java\lib\ext
sun.boot.class.path D:\java\jdk1.7.0_72\jre\lib\resources.jar;D:\j
ava\jdk1.7.0_72\jre\lib\rt.jar;D:\java\jdk1.7.0_72\jre\lib\sunrsasign.jar;D:\jav
a\jdk1.7.0_72\jre\lib\jsse.jar;D:\java\jdk1.7.0_72\jre\lib\jce.jar;D:\java\jdk1.
7.0_72\jre\lib\charsets.jar;D:\java\jdk1.7.0_72\jre\lib\jfr.jar;D:\java\jdk1.7.0
_72\jre\classes
java.vendor Oracle Corporation
file.separator \
java.vendor.url.bug http://bugreport.sun.com/bugreport/
sun.io.unicode.encoding UnicodeLittle
sun.cpu.endian little
sun.desktop windows
sun.cpu.isalist amd64


-PROVIDERS-
prov[0] = SUN version 1.7
prov[1] = SunRsaSign version 1.7
prov[2] = SunEC version 1.7
prov[3] = SunJSSE version 1.7
prov[4] = SunJCE version 1.7
prov[5] = SunJGSS version 1.7
prov[6] = SunSASL version 1.7
prov[7] = XMLDSig version 1.0
prov[8] = SunPCSC version 1.7
prov[9] = SunMSCAPI version 1.7
prov[10] = JCP version 2.0
prov[11] = Crypto version 2.0
prov[12] = RevCheck version 2.0
prov[13] = JTLS version 2.0

-JAR VERSIONS-
D:\java\jdk1.7.0_72\jre\lib\ext\asn1rt.jar build 0.0.0 version 0.0
D:\java\jdk1.7.0_72\jre\lib\ext\ASN1P.jar build 37538 version 2.0
D:\java\jdk1.7.0_72\jre\lib\ext\forms_rt.jar build 0.0.0 version 0.0
D:\java\jdk1.7.0_72\jre\lib\ext\JCP.jar build 37538 version 2.0
D:\java\jdk1.7.0_72\jre\lib\ext\JCPinst.jar build 37538 version 2.0
D:\java\jdk1.7.0_72\jre\lib\ext\JCPRequest.jar build 37538 version 2.0
D:\java\jdk1.7.0_72\jre\lib\ext\JCPxml.jar build 37538 version 2.0
D:\java\jdk1.7.0_72\jre\lib\ext\JCryptoP.jar build 37538 version 2.0
D:\java\jdk1.7.0_72\jre\lib\ext\cpSSL.jar build 37538 version 2.0
D:\java\jdk1.7.0_72\jre\lib\ext\XMLDSigRI.jar build 37538 version 2.0
D:\java\jdk1.7.0_72\jre\lib\ext\JCPRevCheck.jar build 37538 version 2.0

-JCP LICENSE-
company: company LTD
type: client; sign and encrypt
number: CF201-A8000-00VMW-N4
end date: Permanent

-TESTS-
JCP - ok
Crypto - ok
JTLS - ok
JCSP not installed
Get JCP System Preferences - ok
Get JCP User Preferences - ok

Supported charsets:
Big5
Big5-HKSCS
EUC-JP
EUC-KR
GB18030
GB2312
GBK
IBM-Thai
IBM00858
IBM01140
IBM01141
IBM01142
IBM01143
IBM01144
IBM01145
IBM01146
IBM01147
IBM01148
IBM01149
IBM037
IBM1026
IBM1047
IBM273
IBM277
IBM278
IBM280
IBM284
IBM285
IBM290
IBM297
IBM420
IBM424
IBM437
IBM500
IBM775
IBM850
IBM852
IBM855
IBM857
IBM860
IBM861
IBM862
IBM863
IBM864
IBM865
IBM866
IBM868
IBM869
IBM870
IBM871
IBM918
ISO-2022-CN
ISO-2022-JP
ISO-2022-JP-2
ISO-2022-KR
ISO-8859-1
ISO-8859-13
ISO-8859-15
ISO-8859-2
ISO-8859-3
ISO-8859-4
ISO-8859-5
ISO-8859-6
ISO-8859-7
ISO-8859-8
ISO-8859-9
JIS_X0201
JIS_X0212-1990
KOI8-R
KOI8-U
Shift_JIS
TIS-620
US-ASCII
UTF-16
UTF-16BE
UTF-16LE
UTF-32
UTF-32BE
UTF-32LE
UTF-8
windows-1250
windows-1251
windows-1252
windows-1253
windows-1254
windows-1255
windows-1256
windows-1257
windows-1258
windows-31j
x-Big5-HKSCS-2001
x-Big5-Solaris
x-euc-jp-linux
x-EUC-TW
x-eucJP-Open
x-IBM1006
x-IBM1025
x-IBM1046
x-IBM1097
x-IBM1098
x-IBM1112
x-IBM1122
x-IBM1123
x-IBM1124
x-IBM1364
x-IBM1381
x-IBM1383
x-IBM300
x-IBM33722
x-IBM737
x-IBM833
x-IBM834
x-IBM856
x-IBM874
x-IBM875
x-IBM921
x-IBM922
x-IBM930
x-IBM933
x-IBM935
x-IBM937
x-IBM939
x-IBM942
x-IBM942C
x-IBM943
x-IBM943C
x-IBM948
x-IBM949
x-IBM949C
x-IBM950
x-IBM964
x-IBM970
x-ISCII91
x-ISO-2022-CN-CNS
x-ISO-2022-CN-GB
x-iso-8859-11
x-JIS0208
x-JISAutoDetect
x-Johab
x-MacArabic
x-MacCentralEurope
x-MacCroatian
x-MacCyrillic
x-MacDingbat
x-MacGreek
x-MacHebrew
x-MacIceland
x-MacRoman
x-MacRomania
x-MacSymbol
x-MacThai
x-MacTurkish
x-MacUkraine
x-MS932_0213
x-MS950-HKSCS
x-MS950-HKSCS-XP
x-mswin-936
x-PCK
x-SJIS_0213
x-UTF-16LE-BOM
X-UTF-32BE-BOM
X-UTF-32LE-BOM
x-windows-50220
x-windows-50221
x-windows-874
x-windows-949
x-windows-950
x-windows-iso2022jp

фхъ 05, 2014 4:36:04 PM ru.CryptoPro.JCP.tools.Check j
INFO: Jar writing to C:\Users\Potapov\CryptoProJCPInfo.jar

SEVERE: JTLS license check failed: License has expired
javax.net.ssl.SSLException: JTLS license check failed: License has expired
at ru.CryptoPro.ssl.util.c.a(Unknown Source)
at ru.CryptoPro.ssl.ak.a(Unknown Source)
at ru.CryptoPro.ssl.ak.<init>(Unknown Source)
at ru.CryptoPro.ssl.SSLServerSocketFactoryImpl.createServerSocket(Unknown Source)
at JTLS_samples.Server.<init>(Server.java:107)
at ComLine.CheckConfFull.tls(CheckConfFull.java:573)
at ComLine.CheckConfFull.checkTLS(CheckConfFull.java:477)
at ComLine.CheckConfFull.main(CheckConfFull.java:167)
java.lang.Exception: server not running at the test
at ComLine.CheckConfFull.tls(CheckConfFull.java:616)
at ComLine.CheckConfFull.checkTLS(CheckConfFull.java:477)
at ComLine.CheckConfFull.main(CheckConfFull.java:167)
фхъ 05, 2014 5:44:11 PM ComLine.CheckConfFull deleteContainer
INFO: Delete container jcptestserverkey (JCP).
фхъ 05, 2014 5:44:11 PM ComLine.CheckConfFull deleteContainer
INFO: Deleting of jcptestserverkey is completed
фхъ 05, 2014 5:44:11 PM ComLine.CheckConfFull deleteContainer
INFO: Delete container jcptestclientkey (JCP).
фхъ 05, 2014 5:44:11 PM ComLine.CheckConfFull deleteContainer
INFO: Deleting of jcptestclientkey is completed
фхъ 05, 2014 5:44:11 PM ComLine.CheckConfFull logResult
WARNING:
JTLS - FAIL

фхъ 05, 2014 5:44:11 PM ComLine.CheckConfFull main
INFO:
*******************************

фхъ 05, 2014 5:44:11 PM ComLine.CheckConfFull main
INFO:
JCP - OK
Crypto - OK
JTLS - FAIL

Лицензия на JTLS действительно не просрочена (см. в панели)? Серверная лицензия на JTLS нужна, если есть встраивание в веб-сервер, например (или в CheckConfFull, где создается ServerSocket). Если создается только клиентское подключение, то на JTLS лицензия не нужна (не проверяется).