Opened an Atmos project from Nuendo 12 in Nuendo 13 and found that in the VST MultiPanner, panning to rear now produces output to the side channels, and panning to the side outputs to the rear channels. Is there a setting somewhere to fix this? Why did Steinberg make this change with no notification?
Re-check all your connections everywhere.
Also read here: Still in nuendo 12 but - Nuendo - Steinberg Forums
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Nothing has changed between version 12 and version 13. Except that a new 9.1.6 layout has been added for the Atmos renderer. The regular 9.1.6 layout now differs from the one introduced for the renderer. This caused some confusion for me, as the 9.1.6 layout for the outputs (renderer) does not match that of the inputs. 
Conventional 9.1.6 layout
Left, Right, Center, Lfe, Left Surround, Right Surround, Front Left Center, Front Right Center, Side Left, Side Right, Top Front Left, Top Front Right, Top Back Left, Tob Back right, Top Side Left, Top Side Right.
9.1.6 Layout of the Atmos Renderer
Left, Right, Center, Lfe, Left Surround, Right Surround, Side Left, Side Right, Top Front Left, Top Front Right, Top Back Left, Tob Back right, Top Side Left, Top Side Right, Left Wide, Right Wide.
NOTE: Nuendo 13 introduces a new 9.1.6 layout (see below).
Two different layouts, actually.
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Oh yes! I’ve just seen that there’s another 9.1.6 layout. A 9.1.6 (ITU) and a 9.1.6. The latter is the same as the Atmos render. This is new in Nuendo 13.
I had previously saved the “old” 9.1.6 layout in the projects.
Thanks for pointing this out. 
Apologies for posting without:
1: calming myself down
2: doing some research to determine the actual scope of the problem
I have updated the title of the post to correctly reflect the actual problem.
The good news…this does not occur in my Atmos projects that use the Nuendo renderer.
The problem occurs in the projects that use the Dolby external renderer, and it comes from the bed bus (I know this because Objects pan correctly in the VST MultiPanner but tracks routed to the bed do not).
When I create the bed in the ADM Authoring tool, it does not (as far as I can tell) create the Object Bus automatically, so I create a 7.1.2 output bus called bedbus, then use the Add Bed button in the ADM Authoring tool, and choose the bed track for the Source Track and the bedbus for the Object Bus, which causes the object ID’s to be assigned. So far so good.
However, panning a track that is routed to the bed results in incorrect behavior (panning to rear causes output to side speakers and panning to sides produces output to rear speakers).
Panning is correct for Objects.
My workaround will be to swap the routing of the side and rear channels in the bed bus (see screenshot below).
I have tested this by creating an mp4 from the ADM file and the panning is correct when played through an Atmos system.
This is an old problem that has been discussed here many times.
In Nuendo, the order of surround channels and side channels follows the specification of Microsoft Inc. To meet the Dolby requirements for side surround channels and surround rear channels, swap the device ports of the surround channels and the side channels.
In Nuendo, the order of surround channels and side channels differs from the Dolby specification for side surround channels (Lss, Rss) and surround rear channels (Lsr, Rsr). To comply with the specification for the external Dolby Atmos Renderer, swap the device ports for the surround channels and the side channels.
Object busses can also be automatically assigned when using external rendering.
Is this reversal indicated in the manual? And it only concerns 9.1.6? Nothing affected 7.1.4?
Yes, but it seems that in 9.1.6 this is not the case. Or is the problem still just the difference between internal and external Renderers? That would be more likely.
No, the manual just says the usual things about swapping the side/surround channels.
Only the 9.1.6 layout. There are two channel layouts that can be selected when creating a group track, for example: 9.1.6 (ITU) and 9.1.6. The latter is identical to the order in the Atmos renderer…
Steinberg should add the word “Dolby” to the corresponding layouts in Nuendo. Auro-3D and SDDS already have this addition in Nuendo. PT shows the way:
I’m sorry. What exactly are you referring to? That the object busses are not assigned automatically? I can only test this for the internal renderer at the moment, and it works perfectly there.
I thought 9.1.6 was different from 7.1.4 in terms of the order of the rear and side channels. But your expication answers by talking about an order option (basically Dolby VS Microsoft-SB). Now I’m wondering why this isn’t available for 7.1.4.
The problem I described only concerned the order within Nuendo.
The 9.1.6 layout is identical to the one that is used in the internal Atmos renderer. The 9.1.6 (ITU) layout is different. The 7.1.4 layout exists only once and still matches the internal renderer’s channel order.
What’s not correct is the order of the surround and side channels. The 9.1.6 and 7.1.4 layouts still differ from the Dolby layouts outside Nuendo.
That’s exactly what I understood. The 9.1.6 (ITU) corresponds to Dolby. But why is there no 7.1.4 (ITU)?
No. The 9.1.6 and 7.1.4 layouts are identical to the internal Atmos renderer layout.
The 9.1.6 ITU layout is different. It contains channels that do not exist in the Dolby standard.
All layouts differ from the official Dolby layout outside of Nuendo (e.g. the layout in the Dolby Media Encoder). There is currently no layout in Nuendo that corresponds to the official Dolby layout.
Sorry MAS, I obviously don’t understand any of this. Thank you for your patience and kindness.
This is the official Dolby layout. (The picture shows the Dolby Reference Player.) First come the two side speakers (Ls+Rs) and then the surround speakers (Lrs+Rrs).
This is how it looks in Nuendo’s internal Atmos renderer: First the two surround speakers (Ls+Rs) and then the two side speakers (Sl+Sr).
So it’s the exact opposite of Dolby’s products. To add to the confusion, Steinberg uses the same term “Ls” and “Rs”, but means “Left Surround” and “Right Surround”. Dolby also uses “Ls” and “Rs”, but means the side channels. (The channels that Steinberg calls “Ls+Rs” are called “Lrs+Rrs” by Dolby: “Rear Surround” 
.)
This is the well-known problem that these two speaker pairs are swapped in Nuendo. This applies to all layouts!
As long as you only work with Nuendo, there is no problem: the 7.1.4 layout corresponds to the internal renderer layout.
And the 9.1.6 layout also fits.
However, there is a second 9.1.6 layout in Nuendo 13. It has the extension “ITU”. This does not match the layout of the internal Atmos renderer because it contains two channels that do not exist in the internal renderer. (“Front Center” instead of “Wide”.)
In my first project in 9.1.6 I had accidentally selected the “ITU” layout with the wrong layout.
Dietz pointed out that there is a second 9.1.6 layout that matches the layout of the Nuendo renderer.
That I know well. Everything here is based on this inversion (Nuendo follows Microsoft’s layout). On my Apollo x 16, which follows Dolby, I had to invert the rear and sides. Once understood, it’s ok.
This is where it gets complicated, but between you and me, it’s not about Dolby Atmos (or I’m wrong again). I don’t know what this ITU, in fact, is about, and what it can be used for. In the N13 manual, there’s a 5.1.4 ITU. It’s explained that it includes forward angle monitors. But anyway, it’s just a curiosity that you’ve awakened me to. Thanks again for your clarification.
"5.0.2 ITU
This format is used for 3D mixes. In addition to the front channels left, center, and right, and the surround channels left and right, this speaker setup provides top front channels left and right. The front and surround left and right speakers are placed at angles according to the ITU specification.
5.1.2 ITU
This format is used for 3D mixes. In addition to the front channels left, center, and right, the surround channels left and right, and an LFE channel, this speaker setup provides top front channels left and right. The front and surround left and right speakers are placed at angles according to the ITU specification."