Can't execute programs after login but after safemode reboot is OK?

I'm having a really bizarre problem where I've been trying to solve for over a week without much success.

Basically when I login to my compute, I can't execute any programs and I've noticed none of my startup programs are running.

But when I go into Safe mode, then reboot normally and login again everything seems to work as normal?
Could it be a virus reactivating itself or Windows trying to install something in stealth that is messing things up? Or something more innocent at work here?


To give you some background first: I haven't used my computer in over a year because I was travelling a lot. But the computer was running efficiently before and when I turned it on again it was working fine.
I've been using Windows since 3.1 so I consider myself above average when it comes to dealing with Windows issues.

I was using Kaspersky Pure before but it obviously expired so I installed Kaspersky Internet Security with a new subscription code.

I have not run any Windows Update yet on the machine as I don't want add more variables to the situation whilst I'm trying to solve this.

The things I've tried (and failed)

Restore from older disk image backups.
Run HW diagnostics Memory, HDD
Trawled through the Registry for odd entries
Scanned the computer multiple times for virus, rootkits
Ran Gmer
Cleaned up registry via CCleaner
Ran Chkdsk
Ran Autoruns and did a spring clean

I'm convinced it's a s/w issue because it runs normally when I do a normal boot after a Safemode login/exit.

What could it be doing during this normal boot and the next one that is causing this issue?

The only thing left for me to try is
1) Restore File associations to their default (Doubt this fixes anything)
2) Uninstall Kaspersky (I've never had any problems with them all these years I've been using them)
3) Restore to a really really old backup
4) Reinstall Windows.

Any suggestions other than the 4 would be greatly appreciated!

Thanks for the quick response, mitchell65!

Update :
1) The file associate fix didn't work (but I did run in Normal Boot)
2) Creating a new admin user didn't work either. After creating the user in normal boot and tried to login with the new user but it hangs on the Welcome screen after password entry.

I can't seem to run sfc /scannow even though the Trusted Installer service is running.

Malwarebytes did flag a "virus" but it was the Opera Browser Password Tool which I had installed a while back to retrieve some passwords. I've never had any issues with it before but I removed it nonetheless.

I had to reboot the program after the removal of the Tool, and when I login I get a black screen LOL
But I can run process explorer to kill the existing Explorer and start a new one and it logs in.

Unfortunately I still have the same problem.

Yes I double checked to see it was an elevated command prompt (Context Menu -> Run As Administrator).
Still the same service can't start error.

Not sure if it's related but in the normal boot I couldn't see the CBS logs with notepad++, but in safemode it automatically elevated it to show the logs.

I will post the relevant section of the log if you think it's helpful?

My services are as I left it.

I might try deleting the reboot.xml in the winsxs folder and see if that makes a difference as suggested by a comment in this article.

Windows Resource Protection could not start the repair service