Baffling situation

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If I boot tp level 3 and do some command line admin stuff then switch to a user account and continue to open a gui interface my thumb drive is not permitted to mount. At the gui level if I log out as a user and log in as root the drive loads, I can then switch back to a user account and the drive is loaded, my other choice is to go from boot through run level 3 and open the gui as a user and the drive is mounted. I have not checked but assume that I could also go straight to run level 5 and open as a user and the drive would be mounted. What I do as root at run level 3 does not seem to be the problem, it seems that the simple logging in as root is the problem. The choices to work around this are easy enough but I would like to understand why the issue occurs, Have others run across a similar situation?

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