Hello John,
Got your email with your waveform images.
Definite offset of some kind.
DC offset maybe?
Still you've said it sounds ok.
Normally I work on the premise of; if it sounds ok, then it is ok.
I've never had issues with MIDI files and levels, but I don't use them that much, I've only a few bit's of kit that handle GM.
Have a Yammy XG1000 PCI card lying around somewhere, not currently installed in a PC at the moment.
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The Sonic Energy Authority - a sound investment