I'm also delving into the QMBPro mission format: sometime it seems the mission is perfect in FMB, but when you try to load it from QMBPro 409 you get the message the mission is missing or corrupted; I made some early try and failure tests, and at this moment I realize there is some tricky choice about the Red and Blue flights; for example I had some problem using the Kokoda map: I changed the flights to Germans and Russians (r0100, g0100 etc.) but still I wasn't able to load anything; I used notepad and I loaded another Scramble mission using a different map; I just copied and pasted the map/load.ini string replacing the original, and voila, it was loading; after that I adjusted all the paths using FMB to make them coherent with the actual map, changed all the static and moving vehicles and ships again to have consistency about the Kokoda map I'm using, and from then on it started working....
I'm sure there should be some standardized procedure to create a QMBP mission using FMB, but I still I'm not out from trial and errors procedures... I hope to come up with a definitive guide, but I'm not such an expert using all FMB possibilities, and wait if someone more proficient than me can come up with the right solutions!
Anyway, you may have a look at the selectable flight involved using notepad as a start: compare them with a working mission, and see if there are any differences...