Hi!
It is a bit hard to know what the problem could be without seeing it. And I would have to be able to open one of the scenes in question to be sure about anything. If you are not under NDA, could you maybe attach one of the broken scenes and the rig so we could directly look at it?
Usually when a problem is just appearing in a few scenes my guess would be that it is a scene corruption issue, meaning that Maya stored some values wrong while saving the scene and has now trouble reading them properly. But in cases like this, normally all of the animation doesn't work properly anymore not just one controller.
I have some more questions about the issue, if you answer them I might be able to give you better advice on how to fix it.
When you have the Attribute editor open and set a keyframe on the control in question, does the animation curve visibly change on all other keyframes?
How exactly is the controller connected to the blendshape? (Set Driven key, Direct Connection, Math Nodes, etc)
Is there something special about the hierarchy of the rig in those two scenes that isn't present in the other scenes? (Is there something added to the hierarchy, is something constrained to it, is it constrained to something, etc)
Does keyframing the value on this controller influence the values on blendshape targets that are not connected to the control?
Here are some things you could try:
First things first, since this is only happening on a single control. Make sure that there are no keyframes on that control in the rig file you referencing in. I'm sure you already did that, but i just wanted to mention it, because referenced in animation can cause problems with added animation, and during the rigging process accidentally adding keyframes on a control is pretty common.
Also check if there is an overlapping keyframe on that control (two keyframes less that 0.01 frames appart) it's pretty easy to spot those keyframes because they basically look like the curve is in stepped mode. if you find one, delete it.
Now if this is a Scene corruption issue, reimporting the file into a new scene could fix the issue with the following steps:
1) Import your references into the file
2) Select everything in the Scene
3) Export the selection (either as .mb or as FBX with animation)
4) Open a new clean Scene
5) Import the exported file
Now this will cause your references to no longer be references. So I would check if this helps first and if it does, set those scenes asside until you are sure that there won't be any changes in the Reference anymore and then do this process again and finish the Animation.
If this is a calculation issue with the control, one of the following things could help:
Try if the other poses also change if you set a new keyframe on this control on a new animation layer. If it doesn't it's likely a problem with the animation curve itself. And you can try if these approaches help:
1) Just continue animation on that layer and later bake it down.
2) In the graph editor change the curves of this control to stepped and then back to Auto
3) Bake out the values of your animation curve, create a new curve and then reimport the values on that curve.
Change the way that your control is connected to your blenshape. Now this normally only helps if the existing connection is a Set Driven Key, since this type of connection is more prone to miscalculation than others. Normally when connecting a blenshape to a control, the value change is quite linear, so using a setRange node to fit the value of the control to the one of the blendshape also works and is usually faster and more stable.
All of these are longshots but have helped me fix similar issues in the past. There are also other approaches that are even less likely to help, but before I recommend those I would have to try them out on the scene myself.
I hope it helps, sadly with the information given I'm just guessing here.
