Jim, lids and tanks don't "warp" in use, it's always been that way for sure.
I'm willing to bet you've always had vac leakage with the old seal, just really noticed it when to applied the new seal as everything was subject to stricter tolerances now and it was more likely to "hang up" on the less than perfect circle of the tank, which you have now discovered.
The irony of all of this is...If the tank was perfect as was the lid, the thing would not be likely to stay put when you hit speed bumps and such, that lil' bit of side load keeps it secure in the process.
Looking back on all of this, and remembering your "water in the hose" experience, it makes sense, as I never ever heard of a V owner saying that happened to them.
So the question is...Do you still have water in the hose when wrapping up?