Could you elaborate more?
Were you recording like this? Guitar > Amp > Mic > Mic Input on PC > Host??
If you were doing it like that, then yes, you've probably fried your on-board sound card, it's always better to record with a separate USB/Firewire Audio Interface...
EDIT: these are my settings for when i don't have my Audio Interface available at the moment, or the ones i recommend to people when connecting an instrument/microphone directly to a PC to record.