@bill98284 - are you stating you tried to efile and the tax return was rejected....or you paper filed with the Form W-7 and the IRS rejected the application for a W-7? it's not clear from what you wrote.
I didn't think you could efile without the ITIN; it needs to be paper filed....let's see what others state....stay tuned...
Was the paper return sent back to you with the rejected W-7 application ?
Or did the return get forwarded to the IRS and they adjusted the return to MFS ?
What exactly happened ?
# 1 per IRS instructions I sent wife's passport with ITIN application which was rejected.
# 2 filed joint return with temp SSN given to me by Turbo Tax and mailed paper return to IRS.
# 3 got a paper IRS notice discounting wife as joint filer with a $ 3,200 tax bill.
did the IRS give a reason for rejecting the ITIN application? if so, what was it.
# 1 per IRS instructions I sent wife's passport with ITIN application which was rejected. This is an issue you will have to address with the ITIN processing office ... the rejection must have given a reason that can be corrected.
# 2 filed joint return with temp SSN given to me by Turbo Tax and mailed paper return to IRS. What ??? TT doesn't have the ability to hand out a "temp" SSN ... so if you used a fake number on a tax return it will of course be rejected and on a mailed in return corrected.
# 3 got a paper IRS notice discounting wife as joint filer with a $ 3,200 tax bill. Ok ... so the return you mailed in with the "temp" SS# was changed by the IRS ... they dropped the spouse off the return, changed your filing status to Married Filing Separately and recomputed the return. If your spouse had income on the return they probably did not remove any of it ... something else to address later on an amended return.
If you open your return in the program and choose to file separately and complete the rest of the return you should get the same result as the IRS did ... do NOT use the amendment process to do this. Eventually if you get an ITIN or true SS# for your spouse you can amend the return to go back to a MFJ status and your amended return must start with the return as corrected by the IRS in column A of the 1040X.