Interesting to hear from your synopsis that you're a salaried employee with the company and yet, the company treats you like a consultant, and thus, can be taxed as such for this tax season. When you signed the contract, was it made clear that you were accounted for on the payroll? If so, this in effect makes you an employee and it won't be your responsibility to pay whatever taxes you'll pay as a "vendor". If that's not the case, did you have to submit a W-9 form? You can't be paid as a consultant unless you sent it to this company.
Also, check your agreement to see your basis of pay. From what it sounds like, you're paid a flat fee for every given period that will amount to $35k by year's end. If you're only paid for hours billable and assuming you're putting a full day's work, then the company can demand you for time sheets, call reports, etc. My former employer usually held strict policy in this with our development consultants that were billed on an hourly basis per the agreement signed before any projects began. However, one of my colleagues who was paid a fixed consulting fee per every given period, wasn't disputed for the hours he worked and sometimes, he didn't put in the full 8 hours a day working from home as a consultant. Being paid as such usually means that the work is done for the time elapsed no matter the number of hours (act of good faith), much like an employee would.
Another thing is, just because you're reporting to someone who tells you exactly what to do and how to do it, doesn't exactly mean you're an employee automatically. It's normal to have a consultant to be compliant to the core requirements of the job and the duties bestowed as seen fit by the management of the company (otherwise there's a good chance the job won't be done in the best interest of the company). The difference between a consultant and an employee is that a consultant also reports to another entity (whether it's themselves or the company they're hired to), but it depends on the agreement made. That's why I ask if you're officially on the payroll. The IRS can't tax you if you were.
Check out the California Labor Board. I forget the web address, but they can give you a clearer answer to your grievance.
And to answer your thread question, yes I'm self employed.