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.