This isn't really a fix for your situation, but as a work-around you could use
Super Coupons instead of the built-in "Coupon" Order Total. My extension will work to give a 100% discount on a product, by setting it up like this:
Charge Type: Total
Charge Field: -100%
Rule: Product is Product X
It might be cheaper than hiring someone to take a look at this for you, since it's not an easy issue to diagnose. Feel free to take a look at the screenshots and demo site, and if you're interested let me know at
www.getclearthinking.com/contact if you have any further questions.