Ok, been playing the game with no issues, till I deleted the saves an started a new character. I have 48 mods that I have been running with no problems. I am using Wrye Bash, NMM and SKSE, all the latest versions. However, after I create my character, and I am on the chopping block, looking up at the executioner, the cinematic just keeps playing, the dragon fly's around but wont land and just keeps flying. I have uninstalled the game and re-installed it, but the same thing still happens. Any ideas what might be wrong? Is there any information I can provide that I have not already given that might help solve this issue?

Just to expand a bit, I have also re-installed from the disc and not downloaded from steam, but still have the same issue. So sort of completely getting ride of everything, mods, games, files and folders, I am at a loss.

A good clean uninstall/reinstall procedure (from Mark41) Try it: THIS SHOULD BE STICKIED

First do a standard uninstall. (Control Panel\All Control Panel Items\Programs and Features-> Uninstall The Elder Scrolls V: Skyrim)

Next, delete your skyrim folder under C:\Program Files (x86)\Steam\SteamApps\common\

Then delete your Skyrim directory under Documents\My Games (Back-up the folder if you like first)

Then under C:\Users\[Your Username]\AppData\Local\ - Delete the Skyrim folder that is in it.
(You should enable to see the hidden files under windows to delete that folder.) HOW: (View - Options - Folder Options - View - Advanced Settings: Show hidden files, folders and drives)

Go to your Steam folder. Delete the folder named appcache. (Important)

Use Ccleaner after all this (http://www.filehippo.com/download_ccleaner), Go to the Registry tab and hit -
In the Options tab go to Monitoring and uncheck: Enable System Monitoring and Enable active Monitoring

Reboot your computer (Important)

Then install your game again, from scratch. !!!!

*** You don't need to uninstall Steam. ***

First off thank you for the response. I was hoping there would be an easier way than a complete uninstalling an deleting of the folders. My next question is does that go for all the mods as well, or can I save the mods an just re-install them? I would really hate having to spend hours downloading the mods again.

I agree that the clean uninstall and install of the game by Mark should be stickied.

Yes the game should be cleanly uninstalled and then tested with no mods. At least until you get past the issues that you had with the looping scene at the chopping block.

Are all mods downloaded and installed using Nexus Mod Manager. If so the mods are downloaded in the folder you selected for the game and you can get that information by going into the settings option. One of the tabs will show the directory where the mods files gets downloaded to.

I suggest to uninstall all mods using Nexus Mod Manager before uninstalling the game that way when you bring up Nexus Mod Manager hopefully the manager does not think the mods are installed when they are not.

The never ending flying dragon could be mod related.

So, just start the game without mods first, and be careful which mods you install.

All the other stuff, as the other two guys said above.