Are you saying the program isnt capping the SS taxes based on all earnings subject to SS?

Did you enter the Social Security wages and withholding?

Are the W-2 and self-employment income marked correctly for taxpayer or spouse?

Make sure both the schedule C and the W2 are marked properly, i.e. for the same taxpayer, marked t,  or spouse, marked s. I can see how this may happen, but I'm not sure why. Did you try overriding the Social Security tax to the correct amount? Just my opinion.

make sure you have the schedule c checked for the correct person 

That's it of course.  Forgot about no limit on medicare tax.  Thank you so much.

I am saying that but I was wrong.  It was just on going Medicare tax on another $209,000 of self-employment earnings.  Thanks for answering.