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I asked our engineers about this and they said that, if you are doing 2D display, it doesn't use 3D resources (unless you are using Vista). The 3D resources are what are repurposed for stream computations. Most of the performance effect from using the card for displaying as well will likely be with the communication over the PCIe bus, however the commands sent for 2D are relatively small. If you were running video decoding through the GPU at the same time, then it will start using more of that bandwidth as well as the DMA engine.
In our experience, doing even simple 3D or the Folding@Home (which does frequent readbacks from the GPU) don't usually cause much of a slow down in performance on the GPU.
The stream computations that will be least affected will be the computationally denser kernels that have minimal CPU communication dependencies.
It makes sense now. The important message I got is not to use Vista at this point, and use XP-64 bits. The ACML documentation states that it needs a 64 version of windows