It doesn’t matter at all, it’s just a warning that these particular objects could not be scanned. In this particular case, there is absolutely no need to worry – these java jar archives are safe.
Funny thing is: I’ve got two Sony vaio notebooks here which run virtually the same software on top of XP Pro SP1, including Sun Java.
While on the first notebook avast! 4 scans the jar archives without any notice, on the second machine it complains about corruption …
To make things even more interesting: One machine stores several gigabyte of OpenMG encoded music files. In the past avast! 4 did scan these files silently. Now (not sure when this started exactly) it complains about file corruption!