I am not really clear if you are doing the update through the apple update process or through the use of a patchstick. For mine I had tried to put the newer version in recovery after deciding I would like to have a ATV OS 3 partition (prior build of my ATV for Myth had wiped the ATV OS) but the recovery method never worked. The problem I had was the same as yours. Eventually though I went all the way back to a recovery partition with a V1 OS, recovered the ATV to original stock and then let Apple run the upgrades. There appears to be something in the upgrades that properly corrects the remote.
At some version Apple introduced the ability to use non-apple remotes. My theory is that the upgrade performs a firmware upgrade in a manner we do not understand and that letting Apple do the work is the only way that works at this time. Hope this helps. -- To post to this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/atv-bootloader?hl=en
