That would be my guess. Did you recently install any software or update any drivers?
Here is what I would do:
Start your computer normally. Check if problem persists.
If so, try opening a program by finding the .exe, instead of using shortcut. If you right click on a shortcut and select properties, there will be a 'target' field that shows you where the .exe should be.
If problem still persists, I would run some anti-malware tools. AVG, Spybot Search and Destroy, Malwarebytes...
If problem still persists, I would run CCleaner. There is a 'startup' tool that shows you what loads with Windows, and it allows you to remove them. I would disable anything that seems suspicious. Don't delete them so that you can enable them if it turns out to be something you need. Then restart your computer.
If problem still persists, I would personally suggest reinstalling Windows, but if you don't want to do that, you could try just reinstalling some of the programs.