On some plugins “bypass” still keeps them in the chain, and I think that’s because actually switching them off, would change the latency of the plugin chain, and changing latency in the audio chain makes Cubase drop out for a second to re-do all of the plugin latency adjusted calculations.
And if ASIO protection is enabled, things can get even weirder.
So to prove that something is really Cubase related, I typically truly remove, not just bypass or even turn off all 3rd party plugins.