Hi Autoy. Neither of the things you're mentioning are software bugs.
The sub oscillator behavior when oscillator sync is enabled is hardware based, and the expected operation of the OB-6 and P6. Nothing is physically wrong with these synths in this way.
The sub oscillator in the OB-6 is a square wave generated by a flip fop which is driven from the start of oscillator 2's waveshape. When sync is on, oscillator 1's waveshape is retriggered by oscillator 2's frequency. This means that oscillator 2 is retriggered as well, though the frequency of the sub is half that of oscillator 1.
Depending on the oscillators' respective root notes, the sub oscillator may not work consistently from one voice to the next since it is being retriggered at the same time as oscillator 1.
Secondly, the OB-6 will make a click when powered on/off. All of our instruments will do this to some degree. The convention is to power on your speakers/put on your headphones after the synth has been powered on.
The only real changes to the OB-6 OS from 1.0 to 1.1.4.1 are the additional of Poly Chain functionality, added in conjunction with the release of the OB-6 Desktop Module, and the addition of the Velocity Response Curves that we added to the Prophet 6 on it's last OS update.
Cheers.