NTFS I believe has faster file access, plus it uses a different compression technique so you'd actually get more out of your drive space opposed to using Fat32
Really there is no reason to use Fat32 unless you want to run Win98 or something lol.
Regarding the PCI bus....hmm, was it overclocked or something due to raising the system FSB without having a AGP/PCI lock is that what you're referring to?
Other than that, that's just weird that it would decrease like that.