Yes, and it changes my MIDI notes from the original to notes in a different key. It still will not play in the right key. I eventually ended up playing the original file, through modo bass, and recorded it into EZbass and it worked. Still, there should be a way for EZBass to play a note for note MIDI file in the key it was written without having to set a particular key in EZBass.
The same thing started happening to me last night in a session. I have used SD3 for over a year and never had this problem. The MIDI data that keeps disappearing is coming from the the Hard Rock MIDI pack.