This was exactly my experience too, with a passive Epiphone Jack Casady. Tried it at different points in the signal chain, trim pot to zero, even with a buffered tuner right before it. Nothing would prevent the clipping.
I wouldn't count out all of MXR/Dunlop's stuff, though, it seems like these problems are specific to some of the smaller-format bass pedals. I really like the "Echoplex front-end with EQ" concept and after returning my Thump have found exceptional success with a Dunlop Echoplex preamp into a MXR Micro Amp + (the one with active bass and treble).