As you've described it, you made a payment before you efiled. Then you tried to efile and were rejected because your ssn had already been used to efile.
It really doesn't look like the IRS Direct Pay is tied to efiling. If we assume that the IRS systems are mostly correct (Hah!), then you have your answer. It's not the payment, it's an earlier efile. Either you accidentally efiled already (seems unlikely), or the IRS really did get a different return with your ssn.
I suppose it could have been somebody accidentally filing their return with your ssn, but I think that's rare. Unfortunately, there is a type of identity theft out there where people will get your ssn and file a return claiming a big refund (to their address, of course). Oddly enough, the IRS will typically send out those refunds before checking the return against their records. Then they come to you later to get the money back. This does happen enough nowadays that there is a way to appeal and get it cleaned up, but I don't know what it is. Google is your friend here.
Either way, going forward you can close this loophole by getting an IRS Identity Protection PIN. It's all online and takes about 5 minutes. Good luck with all this.
