Time Machine restore leads to strange file permission issues

Question

I've had three Mac laptops over the last 8 years. It all started with an iBook. When I bought my first MBP I used the "migration assistant" to move my files over. I started using Time Machine when it was released. I then upgraded the hard drive on the MBP and used Time Machine to restore the data. Later, I bought another MBP and used Time Machine to transition all of my files.
Each Time Machine restore was flawless.
The problem comes from my most recent hard drive upgrade (details are below). After upgrading the hard drive on the second MBP I did a Time Machine restore, which appeared to complete without incident. However a couple of problems, which are probably related, have cropped up.
After clicking on Firefox.app I get "Profile Missing Your Firefox profile cannot be loaded. It may be missing or inaccessible."
The following message is printed to the console: [0x0-0x31031].org.mozilla.firefox[493]: Error: Access was denied while trying to open files in your profile directory. com.apple.launchd.peruser.501[275] ([0x0-0x31031].org.mozilla.firefox[493]): Exited with exit code: 1
I tried to delete my old profile from ~/Library/Application Support/Firefox and the problem persists. Running /Applications/Firefox.app/Contents/MacOS/firefox-bin -ProfileManager results in the same error.
The file permissions on the ~/Library/Application Support/Firefox directory are:
drwxrwxr-x 2 my_name staff 68B Feb 20 08:31 Firefox
I'm at a loss here because the permissions look correct. When I run the ProfileManager as "sudo" it starts correctly and let's me edit/create a profile for "root".
I've repaired permissions several times, and the disk utility (and Onyx) don't report any problems. A very similar problem occurs for MS Office problems. When I launch Excel (or any other office app) I get an error message saying that the MS Office Database can't be used. Also interesting is that it builds the font cache every time. If I'm not mistaken the font cache and Office database are also stored in profiles, but not under ~/Library
Short story long, after a Time Machine restore some apps can't seem to write profile information, but the file permissions look correct and Disk Utility can't find any problems with my new disk.
Any help or pointers would be great.
Here are the details on the new hard drive:
Capacity: 1 TB (1,000,204,886,016 bytes)
Model: WDC WD10TPVT-00HT5T1
Revision: 01.01A01
Native Command Queuing: Yes
Queue Depth: 32
Removable Media: No
Detachable Drive: No
BSD Name: disk0
Rotational Rate: 5200
Medium Type: Rotational
Partition Map Type: GPT (GUID Partition Table)
S.M.A.R.T. status: Verified
Volumes:
Capacity: 209.7 MB (209,715,200 bytes)
Writable: Yes
BSD Name: disk0s1
Macintosh HD:
Capacity: 999.86 GB (999,860,912,128 bytes)
Available: 668.89 GB (668,892,172,288 bytes)
Writable: Yes
File System: Journaled HFS+
BSD Name: disk0s2
Mount Point: /

Answer 1

You might try the following to repair permissions in your Home folder. Disk Utility does not repair permissions in the Home folder.
To fix Home folder permissions
Open the Terminal application in the Utilities folder. At the command line prompt enter or paste the following command line:
sudo chown -R `id -un`:`id -gn` ~
Press RETURN. You will be prompted to enter your admin password which will not be echoed.