Alright then, let's start from scratch.
Download vba-over.ini from here:
http://www.epforums.org/local_links.php?catid=5
Unzip it and put the .ini file in the same folder where you have the VBA emulator. If you're asked if you want to overwrite a file that's already in there, choose YES.
Go into the rom folder and delete every Tactics Ogre file with these extensions:
.sav & .sgm.
Now start VBA & load the Tactics Ogre rom to begin playing it.
First chance you get in the game, try making a "real" save to see if it works.