[Marty Ward]

I noticed the same thng with the AI running out of resources. I guess since the modders have tweaked the shipbuilding routines now the resources are a little out of balance.
As Emperor Zodd pointed out you should always play with a bonus, I usually play low or medium and get a decent game. Be aware that the AI bonus gives extra resources, research and intel points.
I generally choose the other races manually edit them to account for this. I lower their research and intel abilities a little. I reduce their maintenance cost and increase resource production, usually mineral. This still gives them an advantage in research and intel but not 2-5 times. It also helps them keep large fleets in action.
This is not perfect but I think it will be a huge task to get all AI to use all aspects of the game well. It is so complicated and interlocked that there will always be some comprimises.