It is in the FAQ, it has been for some time:
Quote Originally Posted by FAQ
Q: In custom battles or multiplayer the unit selection is missing units.
A: All of the regionals cause a problem for the custom battle / multiplayer list. There is a special EDU for custom battles / multiplayer in the "...Rome- Total War\EB\mp custom game edu" folder. Rename your campaign EDU then place the EDU from that folder into the "...Rome - Total War\EB\Data" folder. When you want to play a campaign again, switch back to your original EDU.