Did you try panning off each guitar track. Have one to mid-left and one to mid-right?? If not do that. You can also switch the toggle switch for each guitar, say play once with the switch on rhythm, and record it again with the switch on lead. If you don't have a toggle switch, you can adjust the tone knob down for your rhythm guitar, and up for the lead guitar. That should help. If not try messing with your amp. Find two different settings and then record a guitar playing each.