All A.I. factions receive additional scripted financial assistance in the first few turns. Did you remove this section of the script as well? I don't know the reason for this, but I imagine it is to compensate for oversized starting garrisons. After a few turns, it can be reasonably assumed the A.I. will have lost some of these. However, one of the later changes to the script was to give such garrisons only to factions bordering the player. It's possible that the starting financial assistance hasn't been compensated accordingly.

EDIT: come to think of it: the extra garrisons are placed by the start-up script (which runs automatically), while financial assistance comes from the user-activated scripts. Maybe these two don't communicate?

As far as I am aware, the A.I. gets no financial perks other than the scripted assistance and, at VH, a 10,000 mnai per turn bonus.