The fact that your current position is probationary indicates two things: 1) you recently took this new job - that in and of itself is not a reason to deny the loan; and 2) because you're in a probationary period, you can be let go anytime in that time frame for any reason, That's most likely the reason USDA declined to approve the loan.
If you were applying to use the USDA loan, the denial may be because Congress has yet to re-authorize funding. The program is out of money. If that is the case, your bank should have locked you in when money was available. You might ask your congressman or Senators why they are holding it up?