The poorly named Bug 15612 - zimbra corrupts pdf generated by ms office with acrobat distiller documents a general problem that still appears to be happening in 5.0.1.
This is a general problem with any QP-encoded binary attachment. The bug was "fixed" by special-casing PDF files only.
I happened to see two instances of this today. Both are too private for public posting, but one is an Excel file sent from Zimbra Web Client 4.5.10 using Firefox 2.0.11 on a Mac and the other is an SPSS .sav file.
Workaround: Access the messages in question via IMAP. It looks like our legacy IMP webmail installation is going to have to stick around because in some cases (also intenationalization) it is more robust than ZWC.