Are you sure you have the recording properties set right? Go through the recording properties of your soundcard and recording program to make sure everything jives with each other.

When recording, I like to mic my amp if I can have it closed off in another room, and listen to it through the monitors. This however isn't alway's ideal, and can be a hassle. So, I usually use one of my POD's straight into my computers soundcard. I have the soundcard record properties set to record sound comming in from the input I'm plugged into, and the same thing with my recording program. The only time I ever use headphones is when I'm recording vocals (gasp!), and I hate them. So, I can't really help you out much with that.

Hope you get things straightened out. I'm anxiouis to hear those sweet guitars you built!