My W2 had HSA contributions listed in box 14 with the code HSA-EE. It is not shown in box 12 with code W. Why isn't this amount appearing on form 8889 line 2?

[BMcCalpin]

Because your employer did not code the W-2 with the HSA contribution in box 12 with a code of W, like the IRS expects them to.

Box 14 codes are largely not defined by the IRS, so TurboTax can't use them to pick up things like this - TurboTax has no way of knowing what the code refers to.

Before I tell you how to enter this, you have to ask your employer something: "Did you (the employer) remove the HSA contributions from Wages in box 1 on the W-2?"

If the answer is "yes" (HSA contributions were removed so they are pre-tax), please do:

1. Go to the HSA interview (Federal->Deductions & Credits->Medical->HSA MSA Contributions).
2. Go through the interview until you see this screen: "Did [name] put any money into the HSA in 2017?" (see screenshot below). Answer "YES".
3. Note that you may have already seen this screen and answered it, in which case, it won't appear again. Instead, you will look for the screen with the heading "Did your employer tell you about any other contributions?" (see second screenshot below). Answer "YES".
4. Three new lines will appear. Enter your box 14 amount in the last line: "Employer and payroll contributions not reported in box 12 of your W-2."

If the answer is "no" (HSA contributions were not removed so they are after-tax), please do:

1. Go to the HSA interview (Federal->Deductions & Credits->Medical->HSA MSA Contributions).
2. Go through the interview until you see this screen: "Did [name] put any money into the HSA in 2017?" (see screenshot below). Answer "YES".
3. Note that you may have already seen this screen and answered it, in which case, it won't appear again. Instead, you will look for the screen with the heading "Let's enter [name] HSA contributions" (see third screenshot below). 
4. Enter your box 14 amount in the second (bottom) line on this screen, where it says "Any contributions you personally made" - Ignore the "not through your employer".