I can think of two things the Indivision V2 does differently from a real Denise.
The first one is easy to check. The Genlock Audio bit is used to enable Graffiti emulation, I guess that feature should be switched off (not sure what the default configuration is), when doing GenLock thingies.
The other might be a missing feature for the ZD (background indicator) pin in the emulation. Not sure if (and if yes? how) the video toaster would use this pin. This is ZD pin of Denise is connected to pin 14 (called PIXLSW) on the RGB output. Especially for ECS version of the Denise this pin can have a thousand and one different functions, not all emulated. One function is to determine what is background and what is foreground in the Amiga picture.
I admit I don't know how the video toaster works on hardware level, so hard for me to tell what it fails to find exactly at this moment.