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

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...