Buffered bypass pedals can also cause problems. I bought a Germanium Treble Booster from a reputable builder (Blammo! Electronics' Zap Master Treble Booster) and it sounded broken... like "Ice pick of death, speakers gonna blow" broken...
Contacted the owner, Dan and he walked me through checking the bias on the pedal... it was a touch low, but not bad off... ANYWAY, he offered to exchange it, and I said "let me try isolating it first".
I took all pedals off my chain except the Zap Master T.B. Sounded much better...
I started adding pedals back the same order I had them, and it ended up being my Boss TU-2 Tuner. So I recommend any Fuzz (especially Germanium) circuits before anything else... especially buffered bypass... Probably the reason why I've hated every Fuzz I ever tried previously