Lisa has been spot-on with her advice.

The only other thing I can think of (which sure sounds like it doesn't apply in this case) is maybe a Taxpayer vs. Spouse thing?  I think there are two "versions" of the 8889, one for TP and one for SP and you need to make sure the one you're using matches the W-2 with the code W.

Beyond that, just try to line-by-line through the forms to see where things might be going wonky.  I'm stumped.  Maybe try removing the W-2 entirely (not just the code W), removing the 8889, and starting from scratch with both?  Sometimes when ProSeries has an "unexpected behavior" (bug), that's the work-around that helps you get through your day.

Good luck,

Rick