Tax question --- getting the IRS to act?

I am the guy who went in and filed 3 years worth of taxes two weeks ago because the IRS had inputed my income and thought I owed them a lot of taxes and penalties. As it turns out, once I finally filed the 1040's, I have a refund for 2 of the years and I just owe a few hundred for the third year...not the $44,000 the IRS inputed for me. But even though I have now filed the late tax returns and they show I don't own anything like $44,000, the IRS advisor I am working with says it will be 8 to 10 weeks before my returns are processed, and in the meantime the IRS will continue to pursue me for the $44,000. He says I could have my bank account leined, etc, but that if they take my money they will probably refund it at some later date. But that would shut me down as far as writing checks, ect. This guy with the IRS says there is no way he can halt the process until the returns are finally processed by the IRS. Does anyone know of a way that I can get the IRS office where I turned in the taxes (and which AGREES that I owe nothing or little at all) to simply pick up the phone and talk with the collections office? This is crazy!