Are you absolutely certain that FS2 is loading the bak files? It absolutely shouldn't be doing that. Empty your folder of everything but an .fs2 file, edit it in an immediately obvious manner in FRED and then save it. Now try the mission and tell me what you've got. I can't count the number of times I've seen something similar because I was loading the wrong mission
If it really is loading the .bak then you can always simply save twice in FRED.
The second save will overwrite the .bak with the most recent version of your mission.
I have and I did. it works like this:
Step 1: I have a mission, filename "E-m3", in which there is a problem: it is not playing part of a message I thought I had typed. I exit game and turn on FRED.
Step 2: I type in the remainder of the message, notice a ship is in the wrong position so I adjust it. I hit "Save". I minimize FRED.
Step 3: I run FS2, and nothing has changed in the mission whatsoever. The message is untyped, and the ship is in the wrong place. I exit game.
Step 4: I bring up main FS2 folder, look in data/missions and there is E-m3.fs2 along with a file right next to it called E-m3.bak. The .bak was not there before. I delete the BAK data and run FS2 again.
Step 5: The mission works now, the message is typed, and the ship is in the correct position.
So we see that it is in fact, doing something with the .bak files to avoid changes I make to the missions.
Also, if it can't look in VP files, then why when I build a mission off of Inferno's VP, can it play wav files in the VP? My VP is essentially Inferno's with a couple added ships, weapons, and a new stars.tbl. The sound data I copied directly from INF-Main (or the SCP Patch, if it was on there) and put in my own VP. Logically, nothing should have changed. Yet playing the same mission off of my own VP does not yield the wav file playback it did when using Inferno's.