Not certain why Stardock would not respond to paying customers over such a simple issue; however, I will post how I fixed this and send Stardock my support bill.
The issue does seem to be Windows libraries on which WindowFX depends that are overwritten by an update or driver installation. I reinstalled WindowFX and the issue did not repeat until a recent Microsoft update after which I reinstalled WindowFX again and the proper functionality was restored and has remained so.
Perhaps the Stardock coders should deploy these DLL versions into a special folder (similar to the concept of the GAC) not overwritten by updates.
The only libraries we would install and rely on would be some Direct3D (D3DX*) ones, but they are ones which there is only one version of as Microsoft changes the filename each version and our installer wouldn't replace them if they existed.
Perhaps uninstalling some other product deleted them by mistake?
Though we also include them in our program directory so they should be loading up fine even if the OS ones were deleted.
The other case where it would go wrong would be if someone installed WindowFX on 32 bit and copied the install to a 64 bit install as the wrong versions would be included. Likewise if someone were to install the 32 bit libraries to the 64 bit system32 directory.
But in both those cases the animations would simply not work at all. The only explanation for them stopping working over time would be a leak in some component and that would probably be in a video driver. Our usage is very different to a game and we reuse Direct3D devices with very long time gaps in between usage.