Are you using any media other than what was provided? Some crushed coral perhaps? Does the intake tube on each tray have a rubber "O" ring on top? The top tray (the one that goes into the motorhead, shouldn't have one.
It sounds to me like the trays aren't seating properly. I know it means taking apart the filter again, but check to see if each tray sits flat on its bottom, place each one on a table and make sure the slotted bottom isn't bowing up or tray doesn't rock. A concave or convex bottom on just one of the trays can cause a leak and create small blasts of air as the bubbles build up in it.