Rob, one possibility is the trip waste cover, with the lever on it, is not centered on the hole through the tub, and it sits slightly too high. The backside of the lever, where you'll usually find a spring around the lever or an over-center cam moves upwards when the drain is open; it may be hitting the edge of the tub or clamping assembly, which is not allowing it to cam completely into an open position.
Since this has started again after you replaced it, I'd also say you have the barrel on the end of the rod which closes the drain extended too far down. It hits bottom, then forces the lever cover upwards, thus putting it out of position just enough to cause the problem.
Remove the lever cover screws and slide the assembly up & out. Shorten the rod distance a couple turns, tighten the lock nut on the rod, and adjust the screw clamp on the tub to be sure it's centered. Re-install the assembly, and see if that doesn't solve the problem. You may need to do this several times to get the downrod adjustment correct; down far enough to not leak when the trap is closed, but not so far it "bottoms out". Good luck