first time i saw this was with an ez trap and you could see the water do nothing till you poped the cleanout then gush out of the tray put the cap on and the water would stop draining. Strange but does happen
This describes what is happening exactly. You put the cap on for a second the water starts backing up and will eventually come out into the pan. You take the cap off and the water starts gushing down the drain properly again.
From what I can gather, it seems like it is ok to just drill a hole in the cap so the drain vents some?