I've noticed this roof-of-the-mouth burn when the tobacco is wet, and if I puff a bit too much. I think it's just hotter smoke that's burning your mouth.
Maybe try drying the tobacco out before packing the bowl? I have heard that putting some tobacco out on a paper towel for an hour does the trick. Sometimes what I do is pack the pipe, then give it 3 or 4 hours before smoking. The tobacco dries out when I do this and it smokes better (stays lit).
If the tobacco is too wet I tend to puff on it more to get it going, and that makes the bowl hotter.
I think it was Master Yoda who said, "puffing leads to heat, heat leads to burning, burning leads to anger and anger leads to the dark side."