Program folder missing in start menu

[Toolman35]

Had a fake virus alert. I restarted in safe mode and scanned with avg and malware bytes and I noticed then that my spyware blaster along with hijack program was missing. Malware bytes found and removed infected files. When I logged back on all my program files were gone along with most of my desktop items, even IE. Here is the malware log..

Malwarebytes' Anti-Malware 1.50.1.1100
Malwarebytes

Database version: 6341

Windows 5.1.2600 Service Pack 3 (Safe Mode)
Internet Explorer 6.0.2900.5512

4/13/2011 3:41:05 AM
mbam-log-2011-04-13 (03-41-05).txt

Scan type: Quick scan
Objects scanned: 291902
Time elapsed: 9 minute(s), 45 second(s)

Memory Processes Infected: 0
Memory Modules Infected: 0
Registry Keys Infected: 0
Registry Values Infected: 1
Registry Data Items Infected: 3
Folders Infected: 1
Files Infected: 8

Memory Processes Infected:
(No malicious items detected)

Memory Modules Infected:
(No malicious items detected)

Registry Keys Infected:
(No malicious items detected)

Registry Values Infected:
HKEY_CURRENT_USER\SOFTWARE\Microsoft\Windows\CurrentVersion\Run\PxOuRnWAHQGhyii (Trojan.FakeAlert) -> Value: PxOuRnWAHQGhyii -> Quarantined and deleted successfully.

Registry Data Items Infected:
HKEY_CURRENT_USER\SOFTWARE\Microsoft\Windows\CurrentVersion\Policies\ActiveDesktop\NoChangingWallPap er (PUM.Hijack.DisplayProperties) -> Bad: (1) Good: (0) -> Quarantined and deleted successfully.
HKEY_CURRENT_USER\SOFTWARE\Microsoft\Windows\CurrentVersion\Policies\System\DisableTaskMgr (PUM.Hijack.TaskManager) -> Bad: (1) Good: (0) -> Quarantined and deleted successfully.
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Policies\System\DisableTaskMgr (PUM.Hijack.TaskManager) -> Bad: (1) Good: (0) -> Quarantined and deleted successfully.

Folders Infected:
c:\documents and settings\Tim\start menu\Programs\windows restore (Trojan.FakeAlert) -> Quarantined and deleted successfully.

Files Infected:
c:\Documents and Settings\Tim\Local Settings\Temp\ddeslace.dll (Trojan.Agent.Gen) -> Quarantined and deleted successfully.
c:\documents and settings\all users\application data\pxournwahqghyii.exe (Trojan.FakeAlert) -> Quarantined and deleted successfully.
c:\documents and settings\all users\application data\24829748.exe (Trojan.FakeAlert) -> Quarantined and deleted successfully.
c:\WINDOWS\system32\ddeslace.dll (Trojan.Agent.Gen) -> Quarantined and deleted successfully.
c:\documents and settings\Tim\local settings\Temp\jar_cache1316086037071169326.tmp (Trojan.FakeAlert) -> Quarantined and deleted successfully.
c:\WINDOWS\ddeslace.dll (Trojan.Agent.Gen) -> Quarantined and deleted successfully.
c:\documents and settings\Tim\start menu\Programs\windows restore\uninstall windows restore.lnk (Trojan.FakeAlert) -> Quarantined and deleted successfully.
c:\documents and settings\Tim\start menu\Programs\windows restore\windows restore.lnk (Trojan.FakeAlert) -> Quarantined and deleted successfully.

[glc]

This one has been going around lately - the consensus is back up your files, then nuke and pave.

[Kuch]

I'd first check to see if they are hidden. If they are in fact gone, then give this a try.

[Toolman35]

how can I tell if they are just hidden. I know just enough about this stuff to do damage..