I can't make heads or tails from that screenshots. The file types are not clearly visible and they are not sorted...

Suggestion: Select another View mode for your explorer.
-Select "View" from the explorer window's menu bar.
-There should be five view options, of which one ("Large Icons") should be flagged with a black dot. Other five options are something like "Preview", "Small Icons", "List", and at last "List and Information".
-I'm not sure of exact spellings of those in English, since I'm using a Finnish version of Windows XP... regardless, select the lowest of the five options available.
When you have the list/information view selected, select "Order by Type". That's the best way to manage your directories. It puts all executables in one place in the list, all directories in the beginning, and soforth.
Then, take a new screenie...
Even as I can't really see what files you actualy have in the main folder, it's easy to say that you've got too many of them there. Different mod VP files in main folder create heavily erratic behaviour while they are conflicting each other out, having differing tables and so on...
Generally, if you don't really know what you're doing, you should only keep retail files and FS_Open executables in the main Freespace2 folder. Everything else should go to corresponding mod directory. These mods can then be slected to be used, and they don''t disturb each other to hell.