This program does seem to have a few problems in the general design area (I have not looked at every line of code).
Heres a few points to look into.

• this is one of the tasks I used to learn perl :). Since then I have made more advanced versions using relational databases and message threads, it is something you can rewrite again and again as learning progresses.
• warnings and strict save lots of time in debugging and sanity.
• cgi-lib.pl is out of date, use CGI.pm or if you can't maybe CGI_Lite.pm
• why do you use a seperate subroutines.pl?
• why do you have four subs (box1,box2,box3,box4) which seem to repeat most of the functionality of each other. Maybe have one sub and pass it an argument for box number and have interpolation and a few if statements to handle any differences between the boxes.
• your language regex's could be joined and should ignore case ie $in{Comments} =~ /dang|damn|bloody|darn/i
• maybe you could have a common error reporting sub instead of pasting it everywhere you need it
• databases - even DBD::CSV - are good :)
• for a full discussion on a working (but not too complex) bulletin board look at merlyn's column.
• try, try again
• if you have any specific problems, please clarify