If you had already mailed a return you should not have efiled later. That is going to delay your refund. You should have waited for the first return to fully process and then file an Amended return.
As VolvoGirl said, you should not have filed both a paper tax return and an e-filed tax return. The fact that the two tax returns are not the same adds to the confusion. With two different tax returns in the pipeline, there's no telling what the IRS might do. You'll just have to wait and see what happens. It might be another few months before you hear from them.