Your gzipped tar snapshots have truncated filenames. Since it's practically impossible to go through and dig up all the bugs (hundreds of files are affected, e.g., here's a few broken files, notice that they end in ".j" not ".java".
Directory of C:\jutil\jboss\jboss-3.2.1-src\org\jboss\ejb\plugins\cmp\jdbc\metadata
04/24/2003 01:57 PM 9,731 JDBCDeclaredQueryMetaData.j
09/24/2002 11:54 AM 4,964 JDBCEntityCommandMetaData.j
05/19/2002 05:42 PM 5,708 JDBCValuePropertyMetaData.j
3 File(s) 20,403 bytes
I guess no one is trying to build from the snapshot, huh? You could save yourselves the trouble and stop building the snapshot since it's practically worthless. Another possibility is fix the version of tar that is being used. I don't know why it's truncating.