Hi!
I think I was having the exact same problem. Though, I was surprised, that the 'init-patch' (hold down 'manual' and 'write') didn't show the behaviour. Additionally, the 'missing note' seemed to follow a regular pattern, which reminded me a bit of 'paraphonic mode' of my Pro 3 (with one oscilator dialed down to zero).
Solution:
I wasn't using the Ob-6 as a stereo device, because I've just pluged in one channel (the left one).
So, to get rid of the problem, I can either:
- set the global 'mono/stereo' to mono, or
- dial down 'Pan Spread'