Update, I tried to verify laucher jar by the help of jarsigner and it seems to be OK.
$ jarsigner -verify -verbose -certs org.eclipse.equinox.launcher.gtk.linux.x86_64_1.1.100.v20110505.jar
971 Wed Jun 29 09:28:24 CEST 2011 META-INF/MANIFEST.MF
476 Wed Jun 29 09:28:24 CEST 2011 META-INF/ECLIPSEF.SF
5639 Wed Jun 29 09:28:24 CEST 2011 META-INF/ECLIPSEF.RSA
0 Wed Jun 29 08:50:56 CEST 2011 META-INF/
sm 76 Wed Jun 29 09:28:22 CEST 2011 META-INF/eclipse.inf
[entry was signed on 6/29/11 3:28 PM]
X.509, CN="Eclipse.org Foundation, Inc", OU=Digital ID Class 3 - Java Object Signing, O="Eclipse.org Foundation, Inc", L=Ottawa, ST=Ontario, C=CA
[certificate expired on 4/14/12 1:59 AM]
X.509, CN=VeriSign Class 3 Code Signing 2004 CA, OU=Terms of use at
https://www.verisign.com/rpa (c)04, OU=VeriSign Trust Network, O="VeriSign, Inc.", C=US
[certificate is valid from 7/16/04 2:00 AM to 7/16/14 1:59 AM]
[KeyUsage, NetscapeCertType extension does not support code signing]
X.509, OU=Class 3 Public Primary Certification Authority, O="VeriSign, Inc.", C=US
[certificate is valid from 1/29/96 1:00 AM to 8/2/28 1:59 AM]
sm 1445 Wed Jun 29 08:50:56 CEST 2011 about.html
[entry was signed on 6/29/11 3:28 PM]
X.509, CN="Eclipse.org Foundation, Inc", OU=Digital ID Class 3 - Java Object Signing, O="Eclipse.org Foundation, Inc", L=Ottawa, ST=Ontario, C=CA
[certificate expired on 4/14/12 1:59 AM]
X.509, CN=VeriSign Class 3 Code Signing 2004 CA, OU=Terms of use at
https://www.verisign.com/rpa (c)04, OU=VeriSign Trust Network, O="VeriSign, Inc.", C=US
[certificate is valid from 7/16/04 2:00 AM to 7/16/14 1:59 AM]
[KeyUsage, NetscapeCertType extension does not support code signing]
X.509, OU=Class 3 Public Primary Certification Authority, O="VeriSign, Inc.", C=US
[certificate is valid from 1/29/96 1:00 AM to 8/2/28 1:59 AM]
sm 187935 Wed Jun 29 08:50:56 CEST 2011 eclipse_1407.so
[entry was signed on 6/29/11 3:28 PM]
X.509, CN="Eclipse.org Foundation, Inc", OU=Digital ID Class 3 - Java Object Signing, O="Eclipse.org Foundation, Inc", L=Ottawa, ST=Ontario, C=CA
[certificate expired on 4/14/12 1:59 AM]
X.509, CN=VeriSign Class 3 Code Signing 2004 CA, OU=Terms of use at
https://www.verisign.com/rpa (c)04, OU=VeriSign Trust Network, O="VeriSign, Inc.", C=US
[certificate is valid from 7/16/04 2:00 AM to 7/16/14 1:59 AM]
[KeyUsage, NetscapeCertType extension does not support code signing]
X.509, OU=Class 3 Public Primary Certification Authority, O="VeriSign, Inc.", C=US
[certificate is valid from 1/29/96 1:00 AM to 8/2/28 1:59 AM]
sm 620 Wed Jun 29 08:50:56 CEST 2011 launcher.gtk.linux.x86_64.properties
[entry was signed on 6/29/11 3:28 PM]
X.509, CN="Eclipse.org Foundation, Inc", OU=Digital ID Class 3 - Java Object Signing, O="Eclipse.org Foundation, Inc", L=Ottawa, ST=Ontario, C=CA
[certificate expired on 4/14/12 1:59 AM]
X.509, CN=VeriSign Class 3 Code Signing 2004 CA, OU=Terms of use at
https://www.verisign.com/rpa (c)04, OU=VeriSign Trust Network, O="VeriSign, Inc.", C=US
[certificate is valid from 7/16/04 2:00 AM to 7/16/14 1:59 AM]
[KeyUsage, NetscapeCertType extension does not support code signing]
X.509, OU=Class 3 Public Primary Certification Authority, O="VeriSign, Inc.", C=US
[certificate is valid from 1/29/96 1:00 AM to 8/2/28 1:59 AM]
s = signature was verified
m = entry is listed in manifest
k = at least one certificate was found in keystore
i = at least one certificate was found in identity scope
But still getting error mentioned above.