The registry issue is possible, I will explain shortly. But, first things first.
We need to ascertain that your machine's file structure is okay, that is CHKDSK's job, then SFC will check the integrity of those files.
After running each of those scans; remember CHKDSK once, SFC more than once with restarts after each,
you need to check the Start Menu shortcuts to see if there is any improvement.
Now we are getting into the registry question.
This may help: Start Menu All Programs - Add or Delete Shortcuts
with this you can delete, then re-add those problem shortcuts
You can try Icon Cache - Rebuild
If there is still no improvement try booting into Safe Mode
when there pick Last Known Good Configuration
, and press Enter/Return on your Keyboard, and allow Windows to Boot to the normal Desktop.
If no improvement, then your next step would be to preform a System Restore
If there is still no improvement.
Do you recall approximately when this started?
How many programs are "Some", can you list them?
You would need to find out how to un-install those programs, then re-install them. Check to see if there is improvement.
If all of this does not help, the next step would be a Repair Install
Final step is a Clean Install Windows 7