I will need a bit more information before I am able to assist you further. For the first problem, what do you mean exactly when you say 'it will not work"? Does the Joystick Control debugger window recognize the joystick and update the values accordingly, or does it say 'Joystick not equipped'?
For the second issue, make sure that the 'Enable Wireless Searching for NXT' option is enabled in the 'View -> Preferences' menu in ROBOTC; this will allow ROBOTC to search for the NXT via bluetooth and wifi (if you are using it during a competition, you will need to use the Samantha Module to connect via wifi).
If these problems are intermittent between logons, that usually means that there is a program or restriction in place on that particular set of computers that could be resetting the ROBOTC registry values. The only thing I can suggest from the ROBOTC standpoint is to attempt a registry value reset (which will reset them to their ROBOTC defaults); this can be performed by navigating to the 'View -> Delete all registry values' menu option in ROBOTC.
If it is still giving you issues after that, you will need to contact your school's IT department to see if they can find out what the registry restrictions may be.
There are also a couple of links that you may want to look into (below) that could possibly solve the first two problems for you:
Wiki guide on setting up and using joysticks: http://www.robotc.net/wiki/NXT_Using_Joysticks
Wiki guide on setting up the Samantha Module: http://www.robotc.net/wiki/TETRIX_Samantha_Module
Please let me know if you are still having trouble with these particular issues and I will be more than happy to assist you further.
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