I have had no problems with the 5.13 under 98 or 2000 on my Hercules TNT. in fact Quake 3 is now faster on Win 2000 than in Win 98 (about half a frame).
I am having the same problem. I have an IBM 22GXP HDD an AOPEN AX6BC M-Board, The DMA settings are turned on, the motherboard's BIOS detects the drive as UDMA 33, but Win 2000 says PIO mode. I haven't been able to find a solution yet either.