With the main files found intact you now will want to look at what is starting up along with Windows to see if disabling a few items will help clear this up. Simply type msconfig at the Run prompt to bring up the screen for the system utility there.
By checking the selective startup option you then go into the startup group to simply uncheck items found in there. Those can be re-enabled at any time later once the problem is found. By disabling all you then selectively re-enable each item one at a time if needed.
Usually it won't take that long if an item there is the cause. Most are for video, sound, antivirus, and other startups like those. If you have any type of messenger service active that will be among the list seen there. Alos look over any recent software changes.