This never happened in X1 or X2, but started once I upgraded to Platinum. 
 
Let's say I recorded a guitar part from measure four to measure 12 and then stop.  Now, let's say I wanna record something after that on the same track, starting directly on the next measure.  I don't usually start recording directly on measure 13 and go from there.  I like to arm the track, back it up a little to around measure 11 so I can hear a couple of meaures and start PLAYING at measure 13 whatever I'm recording that's new. 
 
The problem is that this process is suddenly muting the music that is "underneath" measures 11 and 12 (you know, because I've started the new recording two measures earlier than when I'm going to play).  And, even if I use the smart tool and chop away the "silent" part of the new track, the part of the original track is kind of faded and still muted. 
 
I hope this makes sense, the way I'm explaining it.  How do I fix this?

Right-click the Record button in the transport module, and choose Sound on Sound record mode instead of Comping.
 
EDIT: To fix the takes you've already recorded, select the muted clip and hit K to unmute it. You can also heal the split that Comp recording created by selecting both halves (or everything in the lane) and Ctrl+clicking in the lower half of one of the clips with the Comp tool that automatically appears when hovering over the lower half of a lane with the Smart Tool.

Are you using punch recording?

Thanks guys!