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I guess I don't understand the purpose of hiring your company, versus you just personally hiring the contractors yourself.

Depending on what exactly happens on the tax returns, if there is any tax savings due to hiring your own company, I agree with the accountant, it would not be allowed.  However, there may not be any tax savings (depending on exactly how you are doing it), in which case it would be okay (but as I said before, I don't understand the purpose of it).