You used the 25th May CVS + build? That probably would explain the problem. I replaced that build 4 days later when I was notified of a problem with it.
What happened is that I replace the ship parsing code for missions as part of my team loadout changes. The new code is much more stringent about catching errors in the mission file and does a better job of telling you where the error is. The problem came when I decided to change the campaign parsing code to use the same function. The code will work perfectly until you change mods. At that point it will parse the table files and then attempt to find the campaign file. At this point it finds a bunch of ships in the FS2 campaign file which aren't in the tables for the mod you're using and promptly complains about them. Since I never tried changing campaigns I never spotted this particular problem.
All I did was remove the more stringent error reporting while keeping the improved parsing routine and posted that in the April 29th build.
It's easy to spot when this build is the problem. It's the only one that will throw up this particular error
Error: Invalid ship type "GTF Myrmidon" found in $Ship Choices: of campaign file
Of course I'm now left with the irony of having spent hours advising ShivanSPS how to avoid big problems with his torrent only to go and cause a rather big one myself
