rnranimal said:

...Then I tried a 2 two-sided LDs and on each one, side one recorded fine, but side two on each had numerous samples which didn't match up.

The laser lens has different tracking settings for each side, so (for your player, as one of mine) when you play side "A" you have no problems, while playing side "B" there are problems (quite surely tracking issue).

If you use the player only to capture, you should not use the autoreverse, but play each laserdisc side on side "A" - when finished to capture the first side, just eject the disc, manually reverse it, and play the other side on side "A" again.