I've noticed that when I first run a project, the FPS drops pretty low for the first few seconds, and then it gets back to 59-60 FPS. There aren't that many events running "At Start of Layout".
I have quite a few objects which are not in use yet, so I just drag them off screen and select the "Destroy outside layout" behaviour. Could this be part of the problem, or does this happen often in larger / complex games?