Beginning with netscape-communicator-4.72 on ia32 Linux the email client doesn't compact folders anymore; i.e. moving one email from Inbox into a separate one makes the message appear in the separate one, but also leaves a "deleted" copy in the Inbox folder. Selecting "File->Empty Trash on Local Mail" or "File->Compact All Folders" from the menu doesn't help. This is especially annoying if one is sharing MBOX folders between e.g. Emacs and Netscape.
Hm... testing here seems to indicate that 'compact all folders' only compacts the *current* folder; is this what you're seeing?
IIRC (I don't have 4.72 installed anymore because of that bug), it did not even compact the current one, but I may be wrong. Anyway, it left duplicates in the mailfolders with flags which just netscape understands, but not XEmacs.
This is fixed in netscape-4.74-1, which will be in the next rawhide release.