I had this problem ever since I used the "refresh" feature in Windows 8. I "solved" the low fps problem by installing the game normally and then placing a copy of the NavyField folder in a external harddrive and launch it from the external hardrive.
The game will still use the .spr files from your internal harddrive, but use the .exe file from your external harddrive. Every time I log in, my external drive starts blinking, meaning it's being used.
It's the best solution I came up with.