Brad, you might try one more thing, if you haven't already. My large lid vacuum for pint and quart Mason jars works well as is, but I had to put a lid with a couple of holes drilled in it inside the small one (for half-pint jars) and I leave it there. You have to drill the holes in it or it will seal to the actual jar lid, leaving you with both lids on the jar. It's used as a spacer.
Also, have you tried putting the jar, lid, and lightly-screwed-on ring (not real tight) into a F/S canister, then vacuuming the canister? When you release the vacuum on the canister, the jar should seal.
Occasionally a lid will pop up for me too. I usually leave the jars on the counter or in the fridge and check them after a day or so to make sure they stay sealed. Sometimes they just won't stay sealed with that particular lid, but another one might work. And sometimes it's just a matter of turning the lid before trying again. Make sure the rims of your jars are not damaged too.
Rita