paperwork is a big issue with the admissions office. If it is a transcript problem, the best thing is to wait a week or two after they should have received it, then give them a booster call to make sure they put that issue near the top. Also, if they have lost it (they did with mine last year), you will have time to send a new one.
as for nominations, that is usually an issue with the congress-to-admissions connection. it will get there eventually.