I didn't replace my motherboard, I changed CPU's, but perhaps more importantly, removed my network adapter. I have not put the network adapter back in the system, because I don't really need Ethernet connectivity for a system that old, so I cannot say for sure that there wasn't some conflict between the GUS and the network adapter. Although, for a while they coexisted harmoniously and the problem only "suddenly appeared".
WinXP : PIII 1.4GHz, 512MB RAM, 73GB SCSI HDD, Matrox Parhelia, SB Audigy 2.
Win98se : K6-3+ 500MHz, 256MB RAM, 80GB HDD, Matrox Millennium G400 MAX, Voodoo 2, Waveforce 192XG.
DOS6.22 : Intel DX4, 64MB RAM, 1.6GB HDD, ELSA Winner 1000PRO, GUS 1MB, SB16.