Can you or someone share any bad experience with publisher regarding the choice of game engine?

If the publisher really interest about which engine you use, I don't think you can lie to her.

Popcap engine is not really an high-end engine but the developers made successful game and money with it.

I think experiences publisher is not blind, if your idea has potential to create the next big hit like Bookworms and Insaniquarium (just an example), the engine bias will be simply wash away.