Safe mode effectively locks out many of the Windows services and some hardware drivers plus other bits and bobs. What might be worth doing in safe mode is looking at the Windows services (Start -> enter "services.msc") and if you can, take some screenshots of the services and those which are started. Reboot in normal mode and take some screenshots again. this time you should notice there are far more, leastways, I hope that would be the case. You might then need to go through each list and look for the ones which might belong to third-party apps you've installed and stop the ones that run in normal mode but which weren't running in safe mode.
The point I'm making is that there could be one or more services which are pulling down your compile but that's purely conjecture on my part. Another thing to look at is to stop any AV program you might have running as they are suspects but not always.
I can't recall but did you reinstall the Arduino IDE and possibly download the latest version?
As safe mode worked that suggests to me there could be either a Windows service or some hardware driver that could be contributing to the compilation time. In the past, I've found it a laborious job trying to hunt down the offender. I don't know the IDE well enough but is there a command line compile option which might throw out some more diagnostics.
I'm sort of glad safe mode worked. I expected it to but the reason is still elusive.