Filed amended return, owing money before receiving initial refund

I am owed a substantial refund but after filing, and before receiving refund, I received add'l 1099 and filed the amended return.  Having an expected refund date of 2-25, I authorized the deduction of what I owed back for 3/1.  The IRS took the money from my account but have still not released my initial refund.  What's going on?