My capital gains from the sale of one stock comes out significantly higher on the final return than the original number on that section of my return. What am I missing?

I'm guessing here: 

You entered a sale of a stock using the "Stocks, Mutual Funds, Bonds, Other" interview and got some number "X".  Now you're noticing that the capital gain reported on the actual income tax return is considerable higher than "X".

If that's all correct then the culprit here is the fact that the capital gains you report can come from more than just your personal sales of securities.  Capital gains are also frequently reported on 1099-DIVs, (LTCG distributions from mutual funds), and Schedule K-1s, as well as other places.  Look at your Schedule D to see what comprises that number.

Tom Young