ok so here is the situation clarification:

It appears that my entire "root/applications/" directory has been copied and pasted into "var/root/applications_ROOT/" with the exception of two programs: installer and snes.

Now, how this has occured I havent the faintest.

secondly, my big idea to fix it, was to move everything back to the original file structure (root/applications) and delete the rogue folder....well that doesnt seem to work. All of my other apps work, but when I try to run either of the other two. I get white screens, and the crash to springboard.

is there something im missing? Maybe a file that links the system to the new application folder or something.

for some reason the phone is not looking in the correct place for apps. If I can get it back to looking at the correct directory, I can delete the old one.

any ideas?