Problems encountered after new user profile created by Windows 7

Question

I am having an issue with my Windows 7 profile and was hoping somebody can help me sort it out.

I am on a domain and the other day after trying to resume after hibernation as I always do, I couldn't log in (said I had the computer locked but would not let me unlock it - I was using the correct pasword). I shut down the computer a couple times and eventually was asked if I want to start up not from my saved session but fresh, which I chose to do. After a long delay, I was finally able to log in. However, I discovered that a whole new profile had been created for my user account. My old profile was [myusername] and the newly created profile was [myusername].[mydomainname].

From what I understand, Windows had difficulty contacting the domain controller which caused it to create a new profile. Naturally, with the new profile, none of my familiar settings etc. were available. What I ended up doing per advice somewhere on stackexchange is to copy the files from my old profile (appdata folder etc) to the new profile. Some things seemed to have been fixed by that (some shortcuts etc. can't remember all) but so much more is broken. The major issues being:

1. I can no longer get to Control Panel or even open Windows Explorer - I receive an error that says "Windows cannot access the specified device, path, or file. You may not have the appropriate permissions to access the item.".
2. I can no longer change file/folder permissions. I get "Can't open access control editor. Access is denied."
3. Fiddler no longer works for me - I believe due to it no longer can install/access its encryption certificate
4. Probably some other badness I either can't remember or haven't as yet formally encountered!

It's been almost a week since this happened so I can't remember everything in order, but I believe that at some point while shutting down, I allowed windows to install a pending update - not sure which one. I was going to try to doing a system restore but can't get into control panel and not sure it would have worked anyway.

I should mention that I tried doing a system file check and chkdsk but no issues were found...

Can anybody shed some light on this nonsense? Is there any way to somehow point this account back to the original profile directory - would that cause more confusion now? I have so many things set up as they should be in my original profile and copying the files doesn't seem to be working as expected.

Thanks for any ideas.