The amount of my medical expenses shown in the deductions section, and in the "estimated breakdown" do not match. Why?

Yes, it is different because of the IRS limit on the Medical expense deduction. You are allowed to deduct only the amount above 7.5 % of your gross income. For example, if your income is $50,000, $3750 will be subtracted from your total  medical expenses. 

In the deductions section, you see the total of what you entered in the medical category. In the estimated breakdown you see the amount you are allowed to deduct.  In other words, the estimated breakdown is your total, less 7.5% of your income. 

Basically, two criteria must be met for medical expenses you be deductible as an itemized SCH A expense.

 - The expenses must exceed 7.5% of your AGI, and only the amount over 7.5% is deductible.

 - The total of all your allowed itemized expenses on SCH A (not just medical expenses) must exceed your standard deduction.