This just underscores how unnecessarily complex our tax laws are, especially regarding corporate tax. I've heard that in many cases nobody, including the accountants and IRS, is really sure exactly how much tax a corporation owes. It depends on how the various laws are interpreted.
One thing really bothers me about the IRS. They always wait a couple of years to tell you about an error on your return just so they can collect more in interest and penalties. There should be a statue of limitations of maybe 3 months after you file your return. If you haven't heard from them by then, then there should be nothing to worry about, ever.
I'm all for getting rid of corporate and individual income taxes anyway. They just make tax collection too complex a matter.