you know what ticks me off about this update, or any update, is how it has an update nag screen. not so much an issue if you plan to update and aren't in sleep mode, but accidentally hitting that button after waking the console up...then a restart.
If your console is in RCM but the computer is not detecting it as such, its most likely a problem with the computer. I would recommend restarting it. I would also advise you to use TegraRCMSmash instead of TegraRCMGUI since TegraRCMGUI has been known to have issues such as this one.