Hi Flycaster,
The main problem with the permissions on Vista, (and not limited to vista) is the fact that setting the permissions on a folder also cascades down the folder tree and sets the permissions on all folders within the top level folder, and so on down the tree.
This makes sense where you are setting permissions for data but is less than ideal when the application folders are concerned.
As the normal situation is for the user/admin to concentrate on Data file permissions the default does make sense.
As this applies to the C:\ drive which is treated as a folder for permissions purposes, changing user permissions on this will also change everything below this level - the whole system
As I understand it The "Trusted Installer" user was added to the Vista system to prevent permissions problems on system files. As it sits at a level higher than a normal administrator it does help the accidental setting of permissions
At the moment however, very few 3rd party software developers are using this system, and so whereas the operating system and probably MS office would survice an accidental change to the permissions to the C:\ drive, (folder), it is likely that 3rd party applications , such as Thunderbird would suffer.
Hope this explains a little as to what I suspect may be the cause of your issue