First, go over this checklist.
Did you file 2553 in the year 2005 or earlier? If you filed it, did you receive an approval from the IRS?
If you answered yes to both questions above, then you should have filed S Corp return instead of C Corp return.
Now, you can take these steps to correct all the errors
1) File amended Corp C return to zero our the effects of Income and Expenses.
2) File amended S Corp return explaining the reason for the amended return.
3) File your amended personal income tax return to disclose the S Corp income (loss).

I cannot tell who actually made the mistake of filing the Corp C return instead of S Corp return. Unfortunately, regardless of whose fault it is, you are at loss. If you had taxable income from your business then you are required to pay taxes and also pay the interest and penalties on the unpaid amount of taxes. The longer you wait to correct, the more you will end up paying.

I would advice that you seek some one elses help if that CPA is not willing to co-operate. You can also reach me at 919-559-2227 or asm361@yahoo.com and I will be glad to help you take care of all the issues.

Good luck and thank you for posting on my blog.