Found root pack 'C:\Games\Freespace 2\DoP_SCP.vp' with a checksum of 0x13c89a38
Found root pack 'C:\Games\Freespace 2\Duke Squad.vp' with a checksum of 0x4406f7c7
Found root pack 'C:\Games\Freespace 2\HellGateIkeya-music.vp' with a checksum of 0x22fc3a8e
Found root pack 'C:\Games\Freespace 2\HellGateIkeya-v1_1.vp' with a checksum of 0x85c63000
Found root pack 'C:\Games\Freespace 2\Internal Conflicts.vp' with a checksum of 0xde9ec77f
Found root pack 'C:\Games\Freespace 2\LoA_music.vp' with a checksum of 0xd5e41aaa
...
Found root pack 'C:\Games\Freespace 2\SotVW.vp' with a checksum of 0x03126046
...
Found root pack 'C:\Games\Freespace 2\TheLightOfAntares-v1_1.vp' with a checksum of 0x9971dd79
These files are not part of a normal FS2 distribution and should be deleted. Never, EVER put mod vps next to the retail ones.
Your problems probably are caused by corrupt savegames, you need to start again with a fresh one.