Projectwise directory missing from Geopak Project Manager

I'm not sure if this is a projectwise or geopak issue.  

We have a peculiar issue where we are unable to see a particular project when searching in GeoPAK's Project Manager dialogue. If we navigate to the root directories, we can see almost every project, except for the ones we started using GeoPAK SS4 on.  This seems to be the only common ground.  We're unable to navigate to the project from the root.

On some machines, we're able to remove the working directory in our user preferences and will place our current working directory into the folder the dgn resides in.  From there, we can navigate backwards to the correct PRJ folder.  If we root back too far, we're unable to go back.

On other machines, our working directory automatically directs to the last project the user worked on.  If they remove the working directory from their user preferences, as soon as they hit ok, it reverts back to the previous project.

This occurs in both Geopak SS2 and Geopak SS4.

Has this happened to anyone or does anyone have a fix or any leads?