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The PAE kernel should be able to address 6GB of RAM. Are you using your usb drive in the way a live CD is used, i. e. instead of a CD, or did you a regular installation on a usb drive instead of a hdd? If you did a regular installation, F11 will write back to your drive. The problem with usb drives is that reading is fast but writing is slow. My guess is that during the hickups, Fedora writes to disk, for instance log files. If you have that much memory, it may be worth trying to create a RAM disk and put /var and /tmp on it. Log and temp files would then be written to RAM, which is much faster than writing on the USB stick.
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