The only thing I can think of is your process is off.
1. Add a user
2. Click the folder on the left hand side you want to protect
3. Check the appropriate user
REPEAT STEP 1-3 FOR EACH USER
Got that. That part works fine ( the first time/first user(s) ) What I (and I think doug200567) are refering to is management day after day. Sorry i wasn't clear enough on that point. There seems to be some inconsistancies with what is viewed, what is changed, and what is deployed and how the exit process sees my actions. See my new post. Maybe it's just my expectations (compared to doing it daily by hand) or misunderstanding what the screens are reporting and why.
Like I mentioned in the other post, we are discontuning the use of WAM in production until we understand what is going on. Following the procedures in the manual we have left (too many) users information unprotected. It took a couple of tries to get it (re) protected. Had to out guess the results using steps that did not seem logical.
We will go back and review the manual and realign our excpectations if necessary
Now that we will be isolated from on-line production we will attempt to document step by step (including screen shots). It may take a llittle longer than we like but we are not software testers and have a full plate with out this.
There was another user on in a different CCup blog that was having challenges with the number of users over 400. We also had the same challenge but set it aside as a possible oversight in procedures on our part as were were "multi-tasking" at the time