> we're a little surprised it writes these bits of text 
> out to the file system instead of storing them in the database.  
> Why was it done that way?
messages and attached files are of arbitrary size.  The design decision
to keep these files in the file system was made by the original author
Ka-Ping Yee over 10 years ago.  The roundup distribution still contains
the paper written by him as the file doc/original_overview.html . 
Unfortunately it doesn't discuss this particular decision.  I can only
guess it was one of the following two reasons: Some of the datebases 
which should be supported by the general hyper database interface are
not very good in storing arbitrary sized blobs of data.  Or getting rid
of old and no longer used attachments and messages without having
rewrite the whole database is a lot easier to implement.  But as I said:
These are wild guesses of somebody not knowing better.

I wonder why you ran into this problem in the first place?
Usually the subdirectory 'db/' of your tracker instance and all
files in it should have the same owner/group and permissions.
If writing to the database succeeds and storing the message 
raises a Permission denied exception then the only plausible
cause seems to be that my assumption above was not true in 
your case.  How comes?