Removed Windows 7 Recovery Malware, But Start Menu Items Still Missing?

so somehow I caught the malware program known as Windows 7 recovery. As per its standard operations it made my computer seem like it was having a bunch of issues, hid all the files on my hard drive, removed my background, etc. I followed a removal guide I found here on bleeping computer and it did rid of me of that annoying malware. A lingering problem I am still experiencing is that all my start menu items are missing. For example there is a folder for Microsoft office, but when you open it it shows as empty, but if I open a Microsoft office file like say a word file the program opens as normal. I have run the unhide.exe file a couple of times, and shutdown my firewall and maleware protection, but to no avail the start menu items still seem to remain hidden.