I am confused, how did you update your 360 from an old firmware to the newest one, without the r6t3 resistor, I recall it blocked you in the middle of the install? Unless you mean you just install Freeboot, in which case, Linux still works for me.
EDIT: I take that back, I never ran Linux with the Kinect update, though I would assume it still works... ran on 8955.
Though this is how I just went to Linux:
Installed Xellous (I didn't care for freeboot or the 360 dashboard at all during this time, but you can install XBR or something(because I know for a fact that works))
Then I burned Gentoo to a cd (not a dvd, don't even think about it)
Then Xellous booted to the cd, and I am in the OS. Then I just installed it by running the ubuntuinstall.sh and bam, I have ubuntu install on my 360 hd

Then grab the sda2 boot disc.
Yep - I just updated Freeboot from 9199 to 12611 using Flash360 and then installed the $systemupdate from the MS web site via a USB, worked without issue. The RT63 resistor stops accidental updates, and gives an E79 error in such circumstances, but Freeboot updates are fine
Not sure what to do, my gut feeling is it either to do with the single layer DVD-R I used (didn't realise I could use a CD-R) or the HDD currently attached (250GB). I might put the OEM 20GB drive in and see if this works / burn a new disc.
Chris.