I don't know that its leak so much as have the things stay secured. When you push them in there's tabs that catch the inside of the hardtop. The gasket provides some tension so they don't rattle around but if the gasket is too thick, you can't push them in far enough for the tabs to catch or the tension actualy cause the vent assembly to come apart. Make sure your vent assembly is secured together...glue, melt the little joiner pins, whatever. Then try to reinstall them. I cut my tabs off just a whisker to make sure they popped out. You may need to evaluate your gaskets and replace if necessary. Self adhesive foam stipping should work.
'05 Rubicon/Sahara 6 spd; '08 Liberty Sport 3.7, auto; '79 J20 360, 4 spd, "Glade8r"; '63 J200 Thriftside, 230 OHC, 3 in the tree; '46 CJ2A s/n 42426; '46 CJ2A s/n 29968, column shift