@Megan Phillips,
My wife and I bought a house in San Antonio last year and the same thing happened where we found out the week of closing that even though we had agreed on $5000 from the seller towards closing costs there was a %2 limit on how much they could contribute. Since the offer price was under 100k, there was a difference of almost $3000 that the sellers did not end up providing. The deal still made sense to us and we moved forward with it (actually at that point we had already signed and my lender had not made us aware of this %2 limit, so it was basically their fault). Needless to say we did not use the same lender for our primary home, which we bought 4 months later in Austin.
I can't understand how this issue hadn't come up in the 10 years the loan officer had been doing business. I considered legal action against the lender but decided to just close on the deal and move forward with our other pending "to do" items.