Worse, for the company, is that unless your arrangement passes various tests (e.g. do you have multiple clients? Who and how decides what you're going to work on, etc.), the IRS can decide you really were an employee and hit the company for that 6.75%, withholding for all of it, and interest.

Normally you have to go through a body shop to get around this (the Senator who was responsible for this change in 1986 seemed to have been working on the behalf of some big ones in his state).