Missing Files due to Malware

ok guys i have another issue with some Malware. I had two clients in the last week come to me with similar issues. one was missing all their files, programs and pretty much everything. the other was missing most of their files and programs. When i say programs, i mean they lost all shortcuts to the applications, even the star menu ones. One machine was XP pro, and the other was Windows 7 Home Premium. i went ahead and ran Unhide.exe, which brought back most of the files, i then ran Malware Bytes from Safe Mode.(with networking to update the definitions) On both devices it found about 5 to 6 items some were trojans etc. further scans came up clean. All the flat files (.docx, .pdf, .jpg etc.) were unhidden when i ran Unhide but several of the application launchers (i.e. the .exe files) are still missing and pretty much everything in the start menu further than one folder deep is still missing. Is there a newer version of unhide i should be trying (i downloaded this one about 8 months ago), or another way to get back the applications? I have run unhide several times with out AntiVirus running per their instruction and have not gotten a different result. It seems there would be a registry fix for this, to reassociate the program files directories with the start menu programs list. Even that would not explain why some of the executable files were simply gone(not hidden).