You can force WHDLoad games to NTSC or PAL by setting the appropriate tooltype in each game (or the global preferences) - no need to fuss with the motherboard.
If you're using the CybergraphX setting or some other patch that allows you to use 56KHz audio modes, turn it off - it messes up native screen modes.
I highly doubt it's a virus.
EDIT: Also make sure your TCP/IP stack and USB stack are offline before starting WHDLoad.
