the same happens to me after at least a few months of using fedora live-usb with a 6 gb persistant-overlay (usually after doing a huge yum install something).
a few reboots seems like a very short lifespan even for a live distro.
also, my xbmc-live-9.10 was running for about two years until i broke down and installed xbmcbuntu-12.04 onto the internal harddrive (but i never apt-get installed anything).
maybe your persistant overlay file is too small for what you are trying to install ?
Last edited by schneidz; 07-02-2013 at 05:23 PM.