I haven't had time to review all your posts, but the thing I was looking for that is definitely a problem is that CEntrance says your Round-trip latency is 769 samples, which is pretty typical for a buffer setting of 256 - maybe just a tad high, indicating there's little bit more "hidden" (unreported driver and USB port) latency than normal. But SONAR says RT is 1195 samples, which makes
no sense for a buffer of 256.
The confusing thing is that having SONAR over-estimate the latency would tend to make it
over-compensate the audio latency, so that it would be
early relative to the MIDI, whereas it appears you MIDI is early. But with that big a discrepancy between actual and reported/detected latency, anything is possible. You could even be aligning the wrong MIDI events to audio transients. You might want to try checking just a single hit to be sure which way it's off.
I would try to get to the bottom of that RT discrepancy with Line 6/Cakewalk support before doing anything else. You may be able to get some semblance of normal behavior out of the system by adjusting offsets, but you shouldn't have to be entering values that big.
If you do want to try adjusting it, though, the first place to start is with a Manual Offset of 769-1195 = -426 (yes,
negative 426 to counteract the over-compensation). And then retest Audio and MIDI sync with Timing Offset at 0.