I'm having the same problem...

I have a Scientific Atlantic 8300HD set-top box which functions both as a digital cable box AND a DVR. Those side selection buttons do not show up under my "Watch TV" activity, but do show under the "Watch DVR" activity that I created (I had to add the 8300HD again as a "DVR" device for this).

It's strange, I get more TV functionality and button options on the Harmony1000 when the 8300HD is set as a DVR device, rather than a set-top device...

So I'm thinking the workaround may be - to get those side buttons displayed - is to rename the "Watch DVR" activity to "Watch TV" and tweek the buttons from there...

I just tried this and it's working out - I have full control of both the tv/set-top and DVR at the same time - I have all the buttons on the screen. It's too bad you need to "trick" the remote this way, but it works.

I really hope that Logitech updates the software soon to reflect the unique interface of the Harmony 1000, rather than the same old software that's also being used for the 880/890's... I used to own an 880 and am finding the 1000 to be slightly more buggy so far.

And yes, I realize it's "just a clock", but I want that on my screen, as in the photos they use to advertise it!! Hoping that firmware update comes soon...