Basically, this is just for me in case I have to look it up again.
The default Asus rom on the Transformer sets the dock layout to US if you pick anything other than the Asus soft keyboard. Why the two are connected is beyond me, but that's what it does.
To fix,
root the tablet,
mount system is r/w,
copy the relevant qwerty kcm mapping (in my case qwerty_gb) from /system/usr/xt9/keychars to /system/usr/keychars
copy the relevant qwerty kl mapping (in my case qwerty_gb) from /system/usr/xt9/keylayout to /system/usr/keylayout
in each directory backup the asusec file and rename your qwerty file to asusec.
Reboot.
Job done.
That's the geekiest post I've written in a while!