Ok, I work in this industry (with the IRS on clients accounts that owe them money), so maybe I can help here. I have a couple clairfying questions. In your first post, you say seperated, are you still legally married (this does matter)?
You said you filed jointly in 2005, and this is where the debt is coming from. When you sent the check, in the memo line, did you write anything? If so, what? (No specifics, just general description.)
You said you received a notice about the "Over payment being applied to 2011" In the top right hand corner of the notice, and the one you received before, there should be a code. Either "CP and some numbers" or "Ltr and some numbers" The ltr code can usually be found on the bottom of the notice if there there is no CP code. Can you tell me what code it is?
If it's easier, or you feel more comfortable, you can PM me.