I'm going to jump in here to say that I've just started experiencing the same thing with my Mac Pro 3,1. I'm running Lion 10.7.3.
The thing is everything worked fine before I upgraded to the ATI Radeon HD 5870 I bought from the Apple Store. I purchased the card to get better OpenCL performance for Final Cut Pro X and Motion 5. One thing I noticed right away was that when the Mac did it's occasional wake up to register with the Time Capsule (Sleep Proxy), the fan noise was much lower and it ran for a shorter length of time as compared to when I had the original NVIDIA GeForce 8800 GT card. With the old card sometimes the fans would run for a very long time and at extremely high speed while registering the with the Sleep Proxy, I would get so concerned about it that I would go and wake the system up to make it stop.
While I was writing this I did another Google search and found this info about Apple's Sleep Proxy Service and how to troubleshoot it. It is written by Stuart Cheshire who works at Apple. Maybe those of you who are also having problems can use the info there to troubleshoot your problem and report back if you find anything useful.
http://stuartcheshire.org/SleepProxy/
Also, I haven't resorted to re-installing the original video card to see if the problem corrects itself. I'd like to see if I can correct it with the new card installed.
