When debug log is enabled the problem doesn't occur during start up. When I disable debug logging the problem starts happening again.
I also noticed that Windows Malicious Software Removal Tool x64 - May 2017 (KB890830) was installed almost at the same time with emsisoft update... I have restored my system to restore point created before any updates were installed and disabled KB890830 in windows update to prevent it being installed.
After rebooting couple of times I have enabled emsisoft auto update. And the problem started to happen once emsisoft was updated. Again, once I enable debug log, the problem disappears. Disable debug log - the problem starts happening again.