I know, we're in the same situation.  We would love to wait for USDA but we can't wait that long for funding.  You should probably look into what down payment assistance is available in your county. 

It does seem like your office is backed up though.  Just because they don't have funding, you should still get a certificate of approval.  If you search the forum (macbook guy)  had a very detailed experience of his usda direct loan.