signing the jar the MANIFEST.MF file is changed and a couple of lines are added for each signed file. These lines are of this kind:
Name: org.apache.log4j Implementation-Vendor: "Apache Software Foundation" Implementation-Title: log4j Implementation-Version: 1.2.15
So, probably, while java plug-in 2 is checking all signature, it scan MANIFEST.MF, looking for all Name: lines, get the file path and look for the corresponding digest line. Of course, when it comes to "Name: org.apache.log4j" it does not find neither the file nor the signature. The message is now clear: the file is really missing.
Name: org/apache/log4j/xml/DOMConfigurator$2.class SHA1-Digest: LxzBa+Ze1FhmRoLDigDVblt9+q8=