My computer is about two weeks old. I did a clean install of Windows 7 64bit on my main hard drive and copied over my files from an external drive. From the very beginning I got permission errors. When I went to install almost every program I wanted, there was at least one or two errors of the "Could not create ... folder, access denied" variety. I fixed them by giving myself permission in the parent folder or by creating the folder myself. This happened even when I ran as administrator. For example, many programs could not make a folder in the start menu (although many could). Recently, I uninstalled my display driver, then when I attempted to re install it again the install kept failing. I tried a lot of different things until I finally checked event viewer (which also wasn't working at first until I changed some permissions) and found the installer for my driver couldn't make a folder in AppData. I created the folder in AppData and gave myself permission and... voilà! my driver install worked. This one puzzled me especially because the installer on the CD that came with my video card worked fine when I first set up the computer, but didn't work when I tried to re install the driver.
Possibly related/unrelated error: In my attempts to install the driver, I activated the default admin account on windows 7, hoping it would have the correct permissions. When logging in, however, it gave me an error that said "Windows cannot load the user's profile but has logged you on with the default profile for the system." along with an error stating that windows could not find the folder "C:\Windows\System32\config\systemprofile\Desktop" I checked that systemprofile folder and no desktop folder exists, which is very concerning.
What files did you copy form the drive? Was it just documents or did you copy a lot more? If you copied more than just your documents, you replaced the files with the files from your drive which have different user rights.
Try re-installing Windows, do not copy any of your old files, and try installing the programs again. Then copy over only the documents, not any system files.