What does your invoice/folio look like? Does it say that you have a room rate of the full $99 and then have a line item indicating a $95 credit? I'd be curious to see a copy of your folio, name and other personal information removed.
I don't see a reference to gift certificates anywhere in the T&C so I feel it is wrong that they should deny you points. My thought is that you can fax a copy of your folio to HHonors with a note on the cover sheet that the points didn't post correctly and that you would like them corrected. I like to communicate with companies via fax so that I have a record of their communication.
Don't give up yet!