It has to do with interrupt allocation. Windows asigns different devices to use different irq's when set up in their aspi auto feature. The stadard PC mode uses more power, but allows for each device to sit on its own irq port, thus not sharing resources and enabling its full functionality on that particular irq. My windows 2000 pro I use is set up as standard PC. Often you can by pass all the BS by going into bios and changing your os type from plug and play to non-plug and play. I would try that first, it generally works quite well.
Daryan