Unfortunately the updater will not run behind the company firewall (I have the same problem with Adobe Acrobat Reader updater).
I have searched the Freescale/Codewarrior website for updates, and I think I have the latest 9S12EXP100 service pack and compiler/IDE updates available. There don't seem to be any specifically for the debugger (ie, comes as part of the IDE).
It seems that, although the debugger knows about and will work with the 9S12XEP100, it does not recognise the 1M48 mask part ID (it would probably recognise one of the other mask set part IDs which can also refer to the 9S12XEP100, but I don't have any chips with other masks to try this out).