Received CP2000 with a large amount owed (Large Self Employment Tax amount)

[mhariush]

I just received a CP2000 notice saying I owe 5,626, which I do not believe I do.

A huge part of that is a $3,536 amount for Self Employment Tax (Schedule 2 Line 4). 

I own a C-Corp and pay myself as an employee of that company on Payroll, so I should not be considered self-employed, why did they add this tax on? 

It is also showing IRS adjusted my reported income tax withheld (Form 1040 Line 25) from 2,685 to $735. My W2 is $3,723.18. But I believe the discrepancy there is that I am in a domestic partnership in California so we are filing as married in California but need to file separately federally but report community income. The community income, as I understand it, divides income and tax payments between the two parties...

Anyone know why on earth they would just suddenly change all that? And How do I proceed with this. I'm on hold with the IRS now, but the phone number they provided states that they can't actually help with specifics...

[Mike9241]

federal law does not require  2 married filing separte returns if you live in a community property state. you can file a joint return  From IRS PUB 555 Community Property page 2. If you are married, your tax usually will be less if you file married filing jointly than if you file married filing separately.

since we can't see any of the documents, the tax returns or IRS notice, I suggest, unless you want to handle this yourself,  you submit the notice to either a tax pro to handle or 

The Audit Defense service is provided by TaxResources, Inc., also called TaxAudit.com, in partnership with TurboTax. If you paid for Audit Defense and you received a notice, call TaxResources, Inc. at 877-829-9695, or report your notice on their website at http://intuit.taxaudit.com/. Do not contact the tax agency until you have spoken to TaxResources. They may contact them on your behalf. if you did not pay for audit defense upfront there will be fees. 

[mhariush]

according to Turbotax we needed to file separately for Federal with Community Property breakdown and a joined California return.