It looks like Microsoft started banning homebrew Xbox 360 (running freeBOOT or XBReboot) from Xbox LIVE. This was of course highly expected to happen any time soon.
There are many ways for Microsoft to detect these modifications, no stealth or anything was implemented (nor is there any will from the dev community to do this considering it would even be possible).
Homebrew and Xbox LIVE don't go together, nor should they probably.