I had this issue but with completely different stuff. My CLD-99 would stop at the end of Side A occasionally. At this time it would also make V-DNR adjustments unnoticeable.
My theory at the time was that a bad TOC read can cause weird issues.
I also attributed it to bad clamping (a more or less always present issue with the 99) assuming that error correction is little to non-existent on TOC reads and the startup slippage could be confusing the motor controller and the chips on the bus that see the TOC.. I've since relieved the slippage issue somewhat and haven't had the TOC problem in years now at this point.
I wish I had noticed this thread earlier, I would have mentioned my issues...