My e file return was rejected. I mailed it, but the irs said they did not receive it. ? But they did receive my payment?

[JohnW15 · Accepted solution]

The IRS typically processes payments associated with tax returns, before the process the returns, themselves.  Paper returns don't show up in their computer records nearly as quickly as eFiled returns, which appear virtually instantaneously. 

So, it wouldn't be unusual for them to have a record of your payment but not your return, at this point in time.