Did u check for audio on all the outputs of the Motu? I had that problem and it was coming out a strange stereo pair.
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SH- 101, BassStation, Alesis Andromeda, Novation Nova, Virus TI 3.0.3 , ATC-1, Waldorf Blofeld... Lexicon, Line 6, Boss.... 96 Point Patchbay 
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