When I was manually turning the plugin power off on some plugins, I was getting glitches/pops in the audio outputs, even though the track was powered off. Were you getting this occur?
I've ended up using another app (Gig Performer) to host most of my plugins and manage patches etc as it is purpose built to deal with complex plugins/routings. I then just route the audio outputs (virtual outputs) to ALK. Has been working well.