You have to indicate family or single coverage, months the HDHP was in effect, etc.. Either the form is filled out incorrectly or the employer overcontributed.  My guess is the former.

Did you put an X in the box on the 1099-SA form to indicate all distributions were use for medical expenses.

all months are populated at $7000 with family coverage.  The employer did not over fund.

Yes, I did that and it flowed properly.  Still being taxed

On the 8889 line two, you didn't put an amount, as the amount is taken from the W2 

Be sure to check the Self or FAmily box in the Smart worksheet below Line 2...not just the box on Line 1 and dont enter anything on Line 2

Did that. All lines are populating at $7000. Still taxing the contribution. 😞

Then you've got something checked somewhere wrong, Delete that 8889 and start over, only check the Family box in the Smart Worksheet below Line 2

that's correct. nothing on line 2.

nope, no entry

Does line 9 of 8889 = W2 contributions?   is it less than line 5?

yes it equal contributions and is less than line 5.

Same $ amount lines 3,5,6,8 ?  

W2 and Form 8889 are both for taxpayer or spouse.  You don't have an "Ownership Designation Mismatch" by chance.     I'm just throwing out ideas, hoping something sticks. 

@dolmana  -  don't leave us hanging ...… did you get your problem resolved?