Ok, then the eqemu_update.pl isn't patching the bots for you correctly. Like I said, it's happened to others. Once it's patched up, the updates should work from this point forward.
First thing to try is resetting the database version to 0. In your DB find the table bots_version. Change that number to 0, and try running the perl script again (option 4 twice). If that still doesn't work, we have to roll up our sleeves.
If you follow this link
https://github.com/EQEmu/Server/tree.../bots/required there will be a list of SQL files (as of this post there are 7).
Grab those SQL files (copy/paste into a blank file with an SQL extension for example) and put them somewhere convenient.
Next, source each SQL into your DB, in order (based on date, newest file last). I usually do this from a mysql command prompt, but you should be able to source them from Heidi.
Once that's done, you may want to change that bots_version table to 9006 (again as of the time of this post). That should get you working.
Alternatively you could check out this link. Similar steps, probably easier to read.
http://wiki.eqemulator.org/p?Manual_..._Bots&frm=Main
If neither of those steps work, we might need to wait for Uleat to take a look at the thread and offer some suggestions. Let us know!