Don't mean to jump in the middle of this as you are working with a lender. It's possible that you need another lender that is more experienced with USDA, however keep in mind that in the current status of this market, it may be difficult to get an offer accepted by a seller using a USDA loan. That in itself is usually an indication of a buyer being less "qualified" vs a buyer who is actually bringing in a down payment.
With you having a short sale just 2 years ago, that may not be enough time for you to fall off the CAIVR list. Typically its a 3 year time period, especially when you are attempting to get a government backed loan, which USDA is.