The program is not adjusting my Social Security Benefits; it's counting the entire amount as income. What gives?

Up to 85% of Social Security Retirement/Disability/Survivors benefits becomes taxable when all your other income plus 1/2 your social security reaches:

Married Filing Jointly - $32,000
Single or Head of Household - $25,000
Married Filing Separately - 0

Look at your federal tax return Form 1040.  On Line 6a will be the total of the benefits you reported from the SSA-1099.  On Line 6b will be the taxable amount of the benefits, if any.

You can view your Form 1040 plus Schedules 1, 2 and 3 at any time using the online editions. Click on Tax Tools on the left side of the online program screen. Click on Tools. Click on View Tax Summary. Click on Preview my 1040 on the left side of the screen.

If you are looking at an income summary screen or review screen those show the full amount as income and lump a lot of stuff together. You need to check the actual 1040 form and make sure it’s right.