I don't THINK you're losing your mind, but...
Vinegar CAN'T hurt a joker valve. It's just rubber, and vinegar doesn't hurt rubber. However, a joker valve will not prevent slow seepage...whatever is left in a hose to run back, will. A brand new joker valve may close tight enough to prevent it, but it only takes a few flushes to loosen it up enough to allow some seepage. And it's not coming from your holding tank...the hose from the toilet from the tank enters the tank at the top...how could any tank contents leap up to run into it. It CAN happen--even with only a 1/4 full tank if you're heeled enough, but there ain't no way it's gonna do it while the boat is upright at rest. Anything that's seeping back into the bowl is coming from the hose. If you have a vented loop in the head discharge, the head discharge hose goes straight up to the loop. Whatever is in the hose between the toilet and the top of the loop when you stop flushing is naturally gonna run back down if it can. Whether you have a loop or not, if you stop flushing as soon as the bowl is empty, that's where the waste is gonna stay till the head is pumped again. The first flush moves a little further...the second one continues to leave waste in the hose to run back into the bowl. Provei it to yourself by replacing the joker valve again and skipping the vinegar...after two people have spent a weekend aboard, the joker valve will start to allow seepage. If you're flushing your toilet completely, it will only be clean water...if you're not, it'll be waste.