Not sure what you mean by domain based mobile account... but here is my 3¢ worth.
First, I use 10.4.5 and ProTools 6.9.2, I never upgraded to 10.4.6 on my production partition. That may be part of your problem, as the latest updates from Apple have in the past broken things with Protools. I know ProTools 7.1 is compatible with 10.4.6, but I can't vouch for 6.9.2 even though it very well may be also.
For my personal LE System, I installed everything onto a dedicated partition and only use 1 user, the admin. By dedicated partition, I mean I set aside a separate partion on my Hard Disk named 'production boot', and I did a fresh install of both Tiger and ProTools including all of the plugins I rely on. Afterwards, I used the Tiger boot disk to save an image of this partiton onto an external drive. Now whenever a new project comes across my desk, I spend the 10 minutes it takes for SystemRestore to wipe the partition and restore the image. This way every new project starts with a virgin ProTools environment. I have been doing it this way for a few years now and it is quite effective.
If you are actually managing ProTools TDM Workstations at a studio, I would avoid separate accounts for each user. In my experience, it never worked quite as advertised and made more work for me in the long run. What I would do is have 2 Accounts, an admin, and a user with limited access.
We would install ProTools under this user account and the users would not be able to administer the machines. This made my life a bit saner since all work was saved to an external scsi and most major problems could be solved by wiping and restoring from a previously saved image.
Ultimately, my advice to you would be to wipe and reinstall fresh, and avoid a mulit user setup if possible.
