re: Amended Tax Return

Just amending a simple return, nothing fancy such as investment income, income other than only job held that year, etc. We've gone to our local IRS office, they stamped the amended return, and we presented that to the lender only to be told they no longer accept the stamp - it must be "processed" through the regional office, ours being Austin, TX. I will add that we now owe money, roughly 10% of what we received from refund. We sent the check with amended return. Since we are not getting any money from them, do you guys think this will shorten the time it takes to process?