I'm Anne. I've been preparing taxes for 27 years and I'll be happy to help you.
First, if you receive a W2, even if it is incorrect, you absolutely may NOT put this income on a Schedule C. This will guarantee an IRS audit.
Your statement that you are an S Corp, and therefore must, by law, file a Schedule C is incorrect. A Schedule C can ONLY be filed by a Sole Proprietor. Since you have an S Corp, you MUST file a Form 1120-S. Please see below:
Please scroll down until you find S Cop.
I understand your arguments re: non reimbursement of employee expenses, but you can't solve that by checking the box next to "Statutory Employee".
You CAN go back to the employer and ask him to issue you a corrected W2 with that box marked.
"I am a home based consultant, doing work at home and the client of the employer's site. I never do work at the employer location. I am given a laptop by the client to do all work."
One of the Common Law Rules is:
Financial: Are the business aspects of the worker’s job controlled by the payer? (these include things like how worker is paid, whether expenses are reimbursed, who provides tools/supplies, etc.)
You stated that they provided the lap top, and that you were a client of the employer's site.
You also stated that you have a signed contract with this employer. I strongly suspect that this contract states that you will be treated as an employee. (Independent Contractors do not sign contracts, since the employer is not covering any payroll taxes for that individual)
I know that this was not the answer you wanted to hear, and for that, I am sorry.
You may try to re-negotiate your contract for this year with the company and see if they will pay you on a 1099 instead of a W2 for what's left of 2016.
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