I have to run explorer.exe manually through task manager with every startup.

[Rhys_4]

I've scanned thoroughly for malware and nothing was detected. I tried SFC scan and It fixed a few things but the problem persists.

 

[Colif]

Try doing a clean boot and see if it still happens, as it maybe a conflict with a start up program - https://support.microsoft.com/en-au/help/929135/how-to-perform-a-clean-boot-in-windows

if it helps, slowly add programs back to find cause.