Do you have copies of the older versions where the frame rate was higher?
You might want to try some experiments. First, after making a backup, I would try first disabling, then deleting all code and see if it makes a difference on the frame rate if its been disabled or deleted. Then I would also try deleting everything from the .cap while incrementally checking the frame rate to try to find if there's anything in particular that deleting helps the frame rate a lot. Then when you finish deleting everything, compare it to the FPS of a fresh .cap.
If you can get the frame rate hit to be there even in a .cap with nothing else in it, maybe someone can help fix it if it's a bug in construct.