Thanks to all responses so far. I finally managed to do basic checks by exchanging the Apple TV with the older one from the bedroom, and the result is:
connecting the Apple TV 2nd gen from the bedroom BV10 to the BV-11 on the very same PUC works flawlessly. The ATV 3rd gen can only be controlled using the Apple TV remote.
Interestingly, when connected to that PUC cable the light on the 3rd gen does respond to the Beo4, but nothing else happens. (Double double check: connecting the 3rd gen to a completely different PUC cable+connected to other connection: same result: no control via Beo4 only with apple remote).
so it does seem a ATV 3rd gen PUC software issue! Again, this started at most just a few weeks ago. I also downloaded the newest ATV PUC software (tourth gen) to no avail.
Interestingly: on the list there is "Apple TV 2nd and 3rd gen", whereas this used to be called "Apple TV" . When I choose to download "Apple TV 2nd and 3rd gen" it does not show up as new item, but seems to remain in my list as "Apple TV".
I then thought: maybe I should first remove existing PUC codes, but did not find how to do that. hhhm ,shall I really try/"risk" a full BV11 factory reset.....?