I found a pretty easy way to make sure the game will recognise your low notes (on standard tuning at least.) go to practice "Vasoline" single note (since most of the song takes place in the first 3 frets of low e) and keep tuning down until you force the game to recognize that first fret. Once that's corrected, it should pretty much be smooth sailing from there on. It ended up being a bit different than the the initial tuning, but the tuner accepted it on my next try anyways.
for drop-d I just screwed around on "Outshined" until there was no problem matching notes as well, but there's probably a better song to do it on. according to my chromatic tuner it barely qualifies as "d" it's so far on the low end, but I'm not having any problems w/ the notes registering aymore, and the in-game tuner accepts it.
Basically, you have to just keep tuning down until all the notes register correctly.
Hope this helps.
I still reccomend anybody having this problem contact customer service and let them know that it's happening.
Last edited by KvnRnld; 10-22-2011 at 01:59 AM.