Update...

I finally got the letter from the IRS on Thursday, and it was vague still as to what the error was. So I decided to call the phone number indicated. After going through a menu of selections and getting through to the department I wanted, I got a recorded message that the next available representative would be an estimated 10-15 minute wait. After being on hold for over 2o minutes I got a live person. After confirming all my information so that she could verify I was whom I knew I was, I asked where the error was on the Schedule SE. The lady I spoke to said that she would put me through to someone that can explain the Schedule SE, in their small business area.

Before I knew it I was on hold again, and the next available representative would be an estimated 10-15 minutes. After another 25 minutes a gentleman responded and I told him about the letter indicating a mistake on the Schedule SE. I asked him what they had for my Schedule SE. He said he didn't have that information only that he explains the form. I told him I use Turbo Tax and it did not indicate there were any errors when I was done. His response was that the IRS doesn't acknowledge (as in guarantee I guess)that program for tax returns and he suggested I contact someone at Turbo Tax. By this time I had been on the phone over an hour.
I knew that I did my return correctly. I told him I have been doing them myself for 30 years, worked for H&R Block one year and am not a stranger to schedule SE.

I asked him why I can't find out where they got a different figure than I did on the Schedule SE. He told me I had to go back to a representative and there I was back on hold again..for another 10-15 minutes which turned out again to be at least 20.

I finally got a person who could tell me the figures on the Schedule SE that they had. I tried to compare with him line by line but they don't have the identical line by line Schedule so I resorted to asking him what figures he had. He got to the social security tax line where I show 0, it indicated I owed, bingo! That was it. And it was whomever did the data entry of my return I suppose who didn't transpose my figures accurately, creating a $3000 tax mistake! I explained how this was not my error but I think I was over this guy's head as he wasn't very familiar with the Schedule SE. So I thanked him, got off the phone and wrote in my response with supporting documents proving I was right. Now it is a waiting game once again and will probably be another 30 days before this is all resolved. Lesson learned. I will never file taxes early ever again.
Every other year I've filed no earlier than a week before April 15th and never had a problem.

Guess it is Murphy's Law. Expect a refund so file early, and get screwed.

I just wonder how many others get letters like this and just don't deal with it because they just assume they must have done their taxes wrong or are just afraid to challenge the IRS. But I hope that people will take the time to find out where the differences are because it may turn out that they are right! Of course it might take 2 hours of being on the phone, but to me it was worth it!