Just a quick update to this in case someone comes across the same problem I faced in the future. After adding the minimote sucessfully it would only let me use the two top buttons. The click and longclick could be used for both top buttons giving me 4 scenes but the bottom buttons didn't work except when pressing both of them to turn off all lights.
Interesting, the same has happened to me.
Luup log from an unsuccessful bottom-left button press ("Electric blanket on"):
06 06/19/12 22:11:01.714 Device_Variable::m_szValue_set device: 170 service: urn:micasaverde-com:serviceId:SceneController1 variable: sl_SceneActivated was: 6 now: 5 #hooks: 3 upnp: 0 v:0x7dd228/NONE duplicate:0 <0x2bf59680>
07 06/19/12 22:11:01.715 Event::Evaluate 5 AUTO_GENERATED scene Coffee start time is false repeat 0/-1 <0x2bf59680>
07 06/19/12 22:11:01.715 Event::Evaluate 6 AUTO_GENERATED scene Bedside lamp to 40% or 60% is false repeat 0/-1 <0x2bf59680>
07 06/19/12 22:11:01.715 Event::Evaluate 7 AUTO_GENERATED scene Electric blanket on is false repeat 0/-1 <0x2bf59680>
06 06/19/12 22:11:01.715 Device_Variable::m_szValue_set device: 170 service: urn:micasaverde-com:serviceId:SceneController1 variable: LastSceneID was: 6 now: 5 #hooks: 0 upnp: 0 v:(nil)/NONE duplicate:0 <0x2bf59680>
06 06/19/12 22:11:01.716 Device_Variable::m_szValue_set device: 170 service: urn:micasaverde-com:serviceId:SceneController1 variable: LastSceneTime was: 1340107703 now: 1340107861 #hooks: 0 upnp: 0 v:(nil)/NONE duplicate:0 <0x2bf59680>
Luup log from a successful top-left button press ("Bedside lamp to 40% or 60%"):
06 06/19/12 22:14:54.430 Device_Variable::m_szValue_set device: 170 service: urn:micasaverde-com:serviceId:SceneController1 variable: sl_SceneActivated was: 5 now: 1 #hooks: 3 upnp: 0 v:0x7dd228/NONE duplicate:0 <0x2bf59680>
07 06/19/12 22:14:54.431 Event::Evaluate 5 AUTO_GENERATED scene Coffee start time is false repeat 0/-1 <0x2bf59680>
07 06/19/12 22:14:54.431 Event::Evaluate 6 AUTO_GENERATED scene Bedside lamp to 40% or 60% is true users:(null) allow:1 <0x2bf59680>
08 06/19/12 22:14:54.431 Scene::RunScene running 6 Bedside lamp to 40% or 60% <0x2bf59680>
08 06/19/12 22:14:54.432 JobHandler_LuaUPnP::HandleActionRequest device: 60 service: urn:upnp-org:serviceId:Dimming1 action: SetLoadLevelTarget <0x2bf59680>
08 06/19/12 22:14:54.432 JobHandler_LuaUPnP::HandleActionRequest argument newLoadlevelTarget=40 <0x2bf59680>
06 06/19/12 22:14:54.432 Device_Variable::m_szValue_set device: 60 service: urn:upnp-org:serviceId:Dimming1 variable: LoadLevelTarget was: 40 now: 40 #hooks: 0 upnp: 0 v:0x8e5308/NONE duplicate:1 <0x2bf59680>
02 06/19/12 22:14:54.433 ZWJob_SendData UPDATE MANUAL ROUTE 3=(nil) <0x2bf59680>
07 06/19/12 22:14:54.434 Event::Evaluate 7 AUTO_GENERATED scene Electric blanket on is false repeat 0/-1 <0x2bf59680>
06 06/19/12 22:14:54.435 Device_Variable::m_szValue_set device: 170 service: urn:micasaverde-com:serviceId:SceneController1 variable: LastSceneID was: 5 now: 1 #hooks: 0 upnp: 0 v:(nil)/NONE duplicate:0 <0x2bf59680>
06 06/19/12 22:14:54.435 Device_Variable::m_szValue_set device: 170 service: urn:micasaverde-com:serviceId:SceneController1 variable: LastSceneTime was: 1340107861 now: 1340108094 #hooks: 0 upnp: 0 v:(nil)/NONE duplicate:0 <0x2bf59680>
Oh, I see what's happened. The buttons have shifted. What used to be on button 3 is now on button 2. I wonder if it's because I'd left button 2 unassigned and the other scenes have bunched up to fill the gaps?
Edit: Looks like the Minimote is sending 1, 2, 3, 4, 5, 6, 7, 8 as top-left-short, top-left-long, top-right-short, top-right-long, bottom-left-short, bottom-left-long, bottom-right-short, bottom-right-long, and that Vera is no longer mapping this to 1, 3, 5, 7 for short presses and 2, 4, 6, 8 for long presses. No idea why.
Edit: Since the continued operation of the Minimote is essential for the WAF, I gave up and excluded/reset/included the Minimote. Unlike Flagstaff, that wasn't sufficient, and the Minimote is still misbehaving, thinking the on buttons are 1, 3, 5, 7 and the off buttons 2, 4, 6, 8. So I dug into the Advanced tab and fooled Vera into thinking I had 8 buttons, and assigned events only to the odd+on buttons and even+off buttons. That seems to have done the trick.
Edit edit: Turns out it was a regression in the private beta I was testing. Not the same issue as Flagstaff.