A tunnel, eh? Sounds like comb filtering to me, though I would expect it to be dropping in overall volume too, not rising. Though if you are recording your parts as stereo tracks that could complicate things.
Did you solo the tracks to hear if they are truly distinct? I suspect the lead track for its four measures contains the lead track and rhythm guitar too. If you are somehow routing the original track into the new one via erroneous routing on an external mixer or recording off the "What U Hear" signal from the sound card, or picking it up the playback onto the new track with a mic, this can easily happen.
Here's what happens -- if you record part B and the track picks up the first part as well, when you play the two tracks together, there is a very slight delay between the first track and its copy. This causes some frequencies to interfere with each other and the blended sound that reaches your ears sounds funny, often like it's all hollowed out or has some very odd filtering going on.
Maybe if you describe your process we can confirm that possibility or rule it out...
