My first guess (as others have alluded to) is that you're running into an income limitation for SEHI.  Here's the first place I'd look:

On your Sch K-1 Wks for this S Corp, right above "Part III" there is a QuickZoom to enter health insurance paid.  That will take you to the K1S Addl Info 1 worksheet and put you at the bottom of the form in a section for "Outside Expenses".  The interplay with the 1095-A is going to be weird so I'd leave box 1 blank "Health insurance premiums paid . . . that were not reported on 1095-A" but the important entry will be box 2, "Medicare wages from this corporation".  Put the number from box 5 of the W-2 here.

Rick