Why are my Windows 7 files randomly being deleted, or diappearing?!?!?

I recently restored my computer, and had all of my downloaded files on a drive, that i plugged into my computer after my pc was in operation.... i double-checked them all once i plugged it in, and they were all there. But now, some are gone! all of the exe's in some folders have disappeared entirely from my pc, but not the readme files. is there some software that goes in and deletes exe files? its really maddening, they cost money! Any help would be appreciated. Oh yeah, one time it only showed my hard drive and the folders directly inside of it, but everything in those folders was completely gone. I restarted my computer hurriedly, and they were all there again. Its strange to me... Anyone else having this problem? (im on windows 7, updated only once since 1.15.11)