Do doctors lose money paying taxes?

Live your dream. Sports medicine is an excellent profession. Even after taxes you'll earn much more then the average person. Your father should be proud of you that you have such high hopes. A Doctor is the highest profession there is. Good luck.

I am having to go back and file my taxes for years 2007?

If 1099s were issued to your boyfriend, they were also issued to the IRS. You have a chance to deduct expenses against that 1099 income to reduce your tax liability. You have to file a return to show the IRS what those expenses are. If you ask the IRS to calculate your tax, they will do so based on information they received from outside sources, such as 1099s and will add on penalty and interest. 1099s belong on a Schedule "C". Try to deduct expenses. Keep receipts in case you get audited.

Can I get in trouble with the IRS for participating in a section 79 plan?

You will not get in trouble. An Approved I.R.S. Section 79 Plan is 100% legal and offers great retirement planning opportunities for successful business owners of both large and small companies.