Frank,
Regarding the PC#1 empty update site list: what OS and version of CCS is this? There was a problem with earlier versions of the eclipse software where the update site list could get wiped out if the installation folder was not writeable. This was one of the reasons we did not want CCS installed into "Program Files" on Windows. This issue was marked as fixed in the eclipse version we use with CCS v6 though.
Regarding the odd license behaviour: The license component is very separate from updates so the odd behaviour you are seeing there is unlikely to be directly related. I guess there could be something far down the stack that is causing both but at the moment I don't' see the relationship. We need need to split off the investigation of that issue into a separate thread if it continues and is causing you a problem.