My SSA-1099 is not showing up in my INCOME. Hence my refund is >$2200 too much. Is this a glitch in the software or is there a backdoor to input it into the form?

Have you entered all of your income?

 

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

 

The benefits from the SSA-1099 box 5 are entered on your federal tax return Form 1040 on Line 6a with the taxable amount on Line 6b

 

Look at your Form 1040 -

You can view your Form 1040 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.