After updating the firmware, have you assigned a setup code to TV and any other  device buttons which you're going to use?  If you haven't assigned a setup code to the TV button, the remote won't accept any other kind of programming.  Press Setup until 2 blinks, Press TV, Enter 0178.  The remote should blink twice.  Then you can go on with the 994 commands.  Each EFC should be put on its own separate button, using all 7 steps.

If you want to e.g. change the device type of the button labeled Audio to one which accepts DVD setup codes, use the 992 command.  However, when you want to make this kind of change, I recommend installing RMIR so that you can see how the remote has been programmed.

The hifi-remote site gets new registrations every day, because it is the primary site for providing custom remotes for Slingbox users.  So I'm pretty sure that the registration routine normally works OK.