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I'm currently running an 8800 GTX and two instances of AoC at the same time. Whichever window is in the foreground is getting 50+fps but the second window goes to 10fps fairly regularly. Is there any settings that'll force the card to keep them both equal?
Not that I'm aware of, they haven't really exposed much of the API yet.
I guess this would be in one of the configuration files, so have a look around your AOC directory for anything that looks like it might be it.
I think this could be due to the operating system's thread scheduler, not the video card or AoC. Windows gives a lot more CPU time to the foreground process than other processes -- its time slices are three times longer. Windows also boosts the priority of the foreground process's threads. Here are a few things you can do to try to equalize things (this is for XP):
1. Try assigning each AoC to a single CPU [edit: half your CPUs] with CPU affinity.
2. Go to Control Panel, System, Advanced, Performance Settings, Advanced, click "Background services" under Processor Scheduling. You wouldn't think it from the name of the option, but supposedly this disables extra-long time slices for the foreground process. The result may be the opposite of what you want -- it may just reduce the FPS of the foreground AoC -- and it may make the system feel sluggish because it increases the length of time slices for all processes -- but it's worth a try.
3. Go to Task Manager, Processes, right click the background AOC, choose "Set priority," and choose AboveNormal or maybe even High (but not RealTime).