Very positive enlightening info from Thad, Product Manager at AJA...
To be clear here, an AJA KONA or Io Express card WILL work in conjunction with Adobe approved nVidia 'CUDA' cards, and the GPU acceleration provided by the Mercury Engine.
When using an AJA card for monitoring, mastering, or other playout, the AJA cards do require that you use an AJA preset. However, those presets allow the Mercury Engine, including GPU acceleration, to do its thing on most file types. There are some uncompressed 10-bit RGB file types that AJA has additional support for, which, will not see the same GPU benefit, but for 99% of Premiere Pro users, their nVidia and AJA cards can work together.
The confusion is created to some degree by the fact that the AJA plugins for CS 5 did have some additional limitations which limited the performance bonus realized by the GPU acceleration when working in an AJA seqeuence in Premiere Pro. However, with CS 5.5, the performance bonus is greatly increased. While it is difficult to make a blanket statement like "4 RT streams" or "4 simultaneous RT effects" due to the number of potential variables that affect the performance of both the AJA plugins, and Premiere Pro, I can say with high confidence that those of you who use both an AJA video I/O card along with an approved nVidia graphics card, will see a great performance bonus relative to using the 'software only' version of Mercury Engine.