I am still not exactly sure what exact pattern this follows, as it doesn't happen for every activated mesh. It may have to do with mesh order within a slot. To reproduce it please replicate the following:

I'm using "spineboy-pro" on 4.2.09-beta
On SETUP, I duplicated head and selected "head2" as the active attachment

Then moved to ANIMATION and keyed the original "head" as active

Now when Free Form Deformation is applied to "head", the editor rejects it. Vertices will key but not move

Another detail: If vertex deformation keys were applied beforehand, or by getting around this bug by swapping around the active meshes on setup, the editor will show the default mesh (blue vertices) when static, but switch to pink vertices when -play- is used (not playback, regular play), and go back to undeformed mesh when -play- stops.
So the data is there, just sort of read-locked when the frame is still.

Another related thing I haven't been able to reproduce is FFD keys being changed/ate up/reset when FFD is already present and meshes within the same slot are swapped around.

I am sorry I can't offer clearer examples for the latter, but as I said, it's rather inconsistent. Hopefully it's just derivative of the first issue and not something else.

Thanks for the support