You know I've seen my share of odd problems, but even I admit this one had me baffled. Here's the situation. I got a laptop that would freeze shortly after starting. Not TOTALLY frozen (I could still move the mouse), I just couldn't do anything. I started with the basics: check for malware and clean out all the temporary files. My two preferred tools for doing this is Malwarebytes Anti-malware and Steve Gould's CleanUp. I do this from Safe Mode (which was working in this case). Found 60-something malware instances and cleaned up about 4 gigabytes in junk files aaaaaaand restart!
So after restarting, the problem still persisted. I moved to phase 2: Windows CHKDSK. This is a built in tool for checking the hard disk for errors. Kinda hard to pull off while you have no access to Windows so it's back to Safe Mode. It ran (on restart), found like 40-something errors, fixed them and then restarted.
No dice, the problem's still there. At this point I can only assume the problem is related to specific software. So I employed the old selective startup trick using MSCONFIG, another built in tool but this time for troubleshooting the operating system. I deactivated every device that wasn't Windows and restarted.
After the restart, this was me....
uTorrent logo. uTorrent is usually a harmless, tiny EXTREMELY POWERFUL torrent downloader. I know, it's pretty great software. However in this instance it was freezing the crap out of this machine. As a test I renamed the program files and restarted and the freeze disappeared. I deleted the files and all is right with the world again.
So what lesson did we learn here? That sometimes even software that's supposed to be there can screw up and turn your PC to crap. :)