I'm trying to get fs2_open 3_6_9RC7 to use missions that I have edited myself. But, for some reason, it continues to load the old versions!

I have removed root_fs2.vp and mv_core.vp after extracting their contents using vpview to ~freespace2/data/ and then deleted all files named *.fs2 in ~freespace2/data and subfolders. But it
still finds missions to load! I've also cleared out the contents of all cache directories I could find (data/missions/backup* and mediavps/data/cache/).
I've tried putting my new missions in my mods directory (mediavps/), into data/missions/, and into data/, all with no success. I still get this old version of the missions being loaded.
Using debug mode, it says the following:
Building file index...
Searching root 'C:\program files\freespace2\mediavps\'
Searching root pack 'C:\program files\freespace2\mediavps\mp-710_adveffects.vp'
Searching root pack 'C:\program files\freespace2\mediavps\mp-710_effects.vp'
Searching root pack 'C:\program files\freespace2\mediavps\mp-710_models.vp'
Searching root pack 'C:\program files\freespace2\mediavps\mv_adveffects.vp'
Searching root pack 'C:\program files\freespace2\mediavps\mv_effects.vp'
Searching root pack 'C:\program files\freespace2\mediavps\mv_models.vp'
Searching root pack 'C:\program files\freespace2\mediavps\mv_music.vp'
Searching root pack 'C:\program files\freespace2\mediavps\mv_textures.vp'
Searching root 'C:\program files\freespace2\'
Searching root pack 'C:\program files\freespace2\smarty_fs2.vp'
Searching root pack 'C:\program files\freespace2\sparky_fs2.vp'
Searching root pack 'C:\program files\freespace2\sparky_hi_fs2.vp'
Searching root pack 'C:\program files\freespace2\stu_fs2.vp'
Searching root pack 'C:\program files\freespace2\tango1_fs2.vp'
Searching root pack 'C:\program files\freespace2\tango2_fs2.vp'
Searching root pack 'C:\program files\freespace2\tango3_fs2.vp'
Searching root pack 'C:\program files\freespace2\warble_fs2.vp'
Searching root 'h:\'
Found 19 roots and 11938 files.
(H is my cd drive, but it has no cd in it. There are no *.fs2 files in any of those roots, as far as I can tell using VPVIEW and windows file search.)
On the briefing screen, it says 'NAME:SM2-05.fs2, mod: 04/16/05 at 20:39.58' and the original mission loads and plays properly. I know that
something is happening because, when I delete 'freespace2.fc2' from ~freespace2/data/missions, I get an ingame message saying it can't find the current campaign.
So can somebody tell me where these missions live? Or how I can get the debugger to print out the whole path to the mission file? Thanks!
By the way, FS2_open is an awesome project.