No witch hunt at all but rather a critical issue on an expensive equipment that needs to be acknowledged and fixed. It would help that someone with access to other DAWs other than Logic and OS 1.4.1 could reproduce the issue.
Other than that, it happens always and regardless of OB-6 global settings and Logic clock settings. I've only tested USB midi but I understand others have reproduced it with DIN midi too.
When I first got the OB-6 module in December and hooked it up to Logic I had exactly the same problems. It just seemed to stop responding to USB. The only solution was to cycle power. It seemed to work better with MIDI DIN. However, the main thing I discovered was that Logic Reset messages included CC#4 Foot Control - this effectively set the OB volume to 0. I disabled that command went back to USB and it's been good since then. I've also been using the clock over USB as well and that seems fine.
I also altered the Global settings which may have made a difference:
MIDI Clock = nss
Clock Port = USB
Parameter Xmit = nr
Parameter Rec = nr
MIDI Control = On
Sysex = USB
MIDI out = MID (not sure if that option will make sense with the keyboard version)
I haven't had any issues with these settings.
As for clock messages I send Logic clock to MIDI Patchbay (by Pete Yandell) and then use MIDI Patchbay to route clocks to all my gear. This could be unrelated but it works better for me this way.
I also did the recalibration thing as I was getting desperate. It took several attempts as the OB-6 kept hanging on the filters. But on the 3rd attempt it worked. Again, probably unrelated.
BTW OB-6 module firmware is 1.1.4.