my program links are gone from menu after using Malware Bytes

HP Laptop, Vista Home Premium.
Ran Makware Bytes, combo fix and Unhide.
After WB my start menu was empty, and all program and document files were empty. I ran Unhide and the most document folders populated, and links to programs returned to start menu. Problem is all links are empty. When I used Hirens, I was able to see all program links and files,
So, how do I restore the program links to the start folder and gain access to my files.
I tried to create a new user, but had the same results