I had a similar problem happen to me last week, whereby all messages were getting tagged with the X-Spam correctly, but if they passed the threshold I set for spam, the seemed to disappear into oblivion. Although I'm not sure where they're going, I think I can at least point you in the right direction to fix.
Check /home/e-smith/files/users/ and in each user folder is a file called ".procmailrc"
In this file it will tell you where each users' spam is being sorted out to. Now, what I did last week was comment out "#" these lines, so that all Spam came through the InBox:
# -------------------------------------------------------------------------
# All mail tagged as spam (eg. with a score higher than the set threshold)
# is moved to the junkmail folder
# -------------------------------------------------------------------------
#:0
#* ^X-Spam-Status: Yes
#$MAILDIR/;junkmail/
From here I could easily use a filter to sort everything with spam headers to whichever folder I like. Hope this helps!
-
s