I'd read about this issue here on the forums, but never experienced anything particularly strange. In my last game, however, I had a race I had a good relationship with, and whom I'd been constantly saving from war with the Drengin (my allies). They were left with two systems outside Drengin range, and spent all their time trying to drop a transport into an undefended planet - this worked on quite a few occassions. The only break in hostilities occured when I called the Drengin off and directed them at whoever I was fighting. This war must have been going, on and off, for more than a decade, and it was simply the inaccessability of the last few Torian systems that kept them alive.
So right in the late game, when the D and I are mopping up the last resistance, the Torians surrender to the Drengin. I had excellent diplomacy, had built or captured all the diplomacy wonders, and was the only person in the galaxy who WASN'T trying to kill the Torians. This confuses me a great deal, and makes maintaining good relations with failing civilisations quite worthless.