Do you know what speed the card is running at? If it's 8x, try running it at 4x.
The VIA KT400 chipset does not always run 8x smoothly.
Go into BIOS CMOS Settings, Advanced Chipset Features, AGP Timing Control.
AGP Mode: If it's 8x or Auto, try setting it to 4x. Restart to see if it runs OK.
If not, go back into AGP Timing Control and disable AGP Fast Write, if enabled.