Okay, I'm editing this post instead of making a new one so at not to bump the thread, but I got it working. It looks like my problems with duplicate mod and .vp loading only happen when my working directory is ~/.fs2_open (even if I call the game's absolute path), which took me all day to notice because while I was trying to troubleshoot I was always sitting in ~/.fs2_open when I ran the game. I guess this precludes my using the launcher, but that's not such a big deal. For now everything seems to be working.
Hey all, I recently decided to get back into the game on my 64-bit Archlinux system. Retail runs fine but any mods, even just the mediavps, crash immediately. Debug log shows mods are being loaded twice (Passed cmdline options: -mod mediavps_3612,mediavps_3612) despite showing up only once in the launcher window and in cmdline_fso.cfg. Then, I noticed that even without mods the retail .vp files are being "Found" and "Searched" twice. Here's the log so it's clear what I mean.
Building file index...
Found root pack '~/.fs2_open/root_fs2.vp' with a checksum of 0xce10d76c
Found root pack '~/.fs2_open/smarty_fs2.vp' with a checksum of 0xddeb3b1e
Found root pack '~/.fs2_open/sparky_fs2.vp' with a checksum of 0x164fe65a
Found root pack '~/.fs2_open/sparky_hi_fs2.vp' with a checksum of 0xa11d56f1
Found root pack '~/.fs2_open/stu_fs2.vp' with a checksum of 0xd77da83a
Found root pack '~/.fs2_open/tango1_fs2.vp' with a checksum of 0x4c25221e
Found root pack '~/.fs2_open/tango2_fs2.vp' with a checksum of 0x86920b82
Found root pack '~/.fs2_open/tango3_fs2.vp' with a checksum of 0x705e8d71
Found root pack '~/.fs2_open/warble_fs2.vp' with a checksum of 0xd85c305d
Found root pack '~/.fs2_open/root_fs2.vp' with a checksum of 0xce10d76c
Found root pack '~/.fs2_open/smarty_fs2.vp' with a checksum of 0xddeb3b1e
Found root pack '~/.fs2_open/sparky_fs2.vp' with a checksum of 0x164fe65a
Found root pack '~/.fs2_open/sparky_hi_fs2.vp' with a checksum of 0xa11d56f1
Found root pack '~/.fs2_open/stu_fs2.vp' with a checksum of 0xd77da83a
Found root pack '~/.fs2_open/tango1_fs2.vp' with a checksum of 0x4c25221e
Found root pack '~/.fs2_open/tango2_fs2.vp' with a checksum of 0x86920b82
Found root pack '~/.fs2_open/tango3_fs2.vp' with a checksum of 0x705e8d71
Found root pack '~/.fs2_open/warble_fs2.vp' with a checksum of 0xd85c305d
Searching root '~/.fs2_open/' ... 3 files
Searching root pack '~/.fs2_open/root_fs2.vp' ... 157 files
Searching root pack '~/.fs2_open/smarty_fs2.vp' ... 10 files
Searching root pack '~/.fs2_open/sparky_fs2.vp' ... 3027 files
Searching root pack '~/.fs2_open/sparky_hi_fs2.vp' ... 1337 files
Searching root pack '~/.fs2_open/stu_fs2.vp' ... 2355 files
Searching root pack '~/.fs2_open/tango1_fs2.vp' ... 32 files
Searching root pack '~/.fs2_open/tango2_fs2.vp' ... 15 files
Searching root pack '~/.fs2_open/tango3_fs2.vp' ... 10 files
Searching root pack '~/.fs2_open/warble_fs2.vp' ... 52 files
Searching root '~/.fs2_open/' ... 3 files
Searching root pack '~/.fs2_open/root_fs2.vp' ... 157 files
Searching root pack '~/.fs2_open/smarty_fs2.vp' ... 10 files
Searching root pack '~/.fs2_open/sparky_fs2.vp' ... 3027 files
Searching root pack '~/.fs2_open/sparky_hi_fs2.vp' ... 1337 files
Searching root pack '~/.fs2_open/stu_fs2.vp' ... 2355 files
Searching root pack '~/.fs2_open/tango1_fs2.vp' ... 32 files
Searching root pack '~/.fs2_open/tango2_fs2.vp' ... 15 files
Searching root pack '~/.fs2_open/tango3_fs2.vp' ... 10 files
Searching root pack '~/.fs2_open/warble_fs2.vp' ... 52 files
Found 20 roots and 13996 files.
I looked around at some random logs from other linux users and never saw this happening, so I figure it's at the root of my problem. It happens the same way for me whether I'm using the 3.6.12 distributed binaries, building from the source in the 3.6.12 release thread, or building from the latest SVN, so I guess it's something stupid I've done on my end, but I'm not savvy enough to figure it out and it's driving me insane. If anyone has any ideas I'd really appreciate the help.