MrSid, I'm sure I've mentioned this before, but "pci latency" issues are not an "AMD" specific problem. Intel i850 and i845 boards also suffer from this problem. Your problem is actually a VIA issue, not an AMD issue. (P4X266 suffers from it as well.)
I think there is a lot of confusion on this issue:
The problem is due to the 133 MB/sec bandwidth limitations of the PCI bus itself and how it behaves when that limit is exceeded. Intel's workaround was simply to limit bandwidth usage to 80 or 90 MB/s. (I can't remember the exact figure at the moment.) VIA's fix was to change the interupt timings to reduce the bandwidth used at any given point. Both solutions (of course) reduce performance. I850 and i845 hard disk benchmarks are, as a result, pretty poor compared to other chipsets.
Some AMD supporting chipsets, nVidia's nForce for example, has no reported "pci latency" issues. I don't know if the Ali and Sis chipsets suffer from this.
The SB Live series of soundcards had driver issues that could cause some serious problems. Even though 133 MB/s sounds like plenty, remember that on all but a very few examples, IDE disk traffic was transfered across the PCI bus. Burst transfer speeds for some drives may require all available bandwidth. (ATA133 can support a transfer rate of 133 MB/s remember.) Add a SB Live playing an audio stream while transfering large files back and forth between the primary and secondary IDE channels and disaster resulted. I'd imagine a raid array would be even worse. (Nvidia got around the problem by moving IDE traffic to a "Hyper Transport" 800 MB/s capable bus.) I personally think that Serial ATA should help with this problem when it becomes available later this year. (If it's not delayed again... )
In no way does the processor itself directly cause this problem.
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I personally generally go with NTFS on my own system for security reasons, but I will say that in a dual boot configuration with Win9x, FAT32 is more convienient as Win9x cannot read NTFS formatted disks.
If you turn off some of the silly Windows 2000/XP disk indexing services, NTFS also improves disk performance compared to FAT32 on large partitions.
I'm not sure if the 4 GB limit is a FAT32 issue or an OS issue. I personally think it's probably an OS issue.
In Eagler's case, I'd probably suggest FAT32 IF he planned on a dual boot configuration where Win9x was heavily used. You *could* set aside a small special partition for Win2k/XP OS itself and format it NTFS. I think I'd probably go with FAT32 though. I've actually had a power failure wipe out an NTFS formatted disk to the point where I had to reformat it.
