With 64bit Linux mplabx don't properly recognise pickit. I made a short post on how to solve it:
http://elco.crsndoo.com/wordpress/2011/ ... bit-linux/ (http://elco.crsndoo.com/wordpress/2011/03/how-to-make-mplab-x-work-properly-on-64bit-linux/)
in short - install parallel to your 64bit jdk one that is 32bit and tell mplab to use that one.
attached the mplab.x beta5 with both pickit2 and pickit3 recognised (host os is Fedora14 64bit)