Call the whichever school you are applying to and let them know of your problem. I never had this problem because at my school we start registering for fall classes starting in April and they do it on an earned hour basis, so seniors with more hours get more time than the other students. As for myself, I am graduating in the fall, so when I told the department that, I was moved to the top of the list and it didn't matter who was already enrolled in the class.
I am not sure how important it is, but I have heard of "conditioned" acceptances where you have to finish the courses that you said you were going to finish. Just keep them informed of any changes like that.
Hope this helps.