I was flying the main FS2 campaign recently and had a similar problem.  I came to "Slaying Ravana" and suddenly my bomber wasn't able to carry bombs.  It seems that the tech room was loading in the Cyclops#short bomb rather than the conventional Cyclops.  I looked the mission up in both FRED2 and FRED2_Open and the team loadout screen doesn't even have an option to select the #short.  I looked at the table files for both the bomber and the weapons and couldn't find any typos or errors that would account for this.  I eventually had to edit the ships.tbl to allow the bomber to carry the #short to get it to work.  I wasn't sure if this was a problem with Open, or if it was with the FS-Port.  I'm using the 2.1 version of the port which includes a change to certain missions, this one included, so I wasn't sure if the Port is at fault, or if its a problem with Open.  Your comment kinda jogged my memory and prompted me to post.
Later!