Are you sure they are mounted correctly? They do have a front/back as well as up/down.
Not remembering the exact front back, but the up down should look sorta like this really cheesy asci art: /\ There is a small tab that should be on top of the boots. The carbs should also be full engaged, pressed nice and snug against the boots, not sticking out at all, ans well as the air cleaners. If this is not so, maybe a quick disassemble to check is in order. Quick enough if you do not have an airbox.