OK it's happening again.

I'm still sending the same CC and it still hapens with "Flip direction" only.

I've noticed that when I send the CC it shows "BYPASS" in the screen for a second and it does the reverse thing. After that, I can not record anymore, because it has been bypassed, but if I send the CC for "REC" the screen shows "R > 0:00" and "D > 0:00".

Any help will be appreciated.

We're having trouble reproducing this.  Are you doubly sure none of your MIDI CC mappings under RCV.CTL in the H9 itself are mapped to BYP, FS1, FS2, or FS3?