I'm seeing this lag too. It seems like the 2nd time you get to the QuickGuide after you've changed the collection you get the right collection.
I'm really liking this as I've played with it over the weekend. I think this will become the flagship feature of the product because its name is Channels, and now control and organization of the "channels" is front and center, and unlike any other product I've seen or remember.
This was because the channel identifier was conflicting. This has been resolved via the pluto-for-channels project. You'll need to update your docker to the latest release to get things fixed.
update your pluto-for-channels docker container
go to your pluto custom channels source and choose Reload M3U and then Redownload XMLTV.
Excellent. Just updated the docker container, reloaded m3u, redownloaded xmltv, and was then able to add 10559 CNN alongside 6030 CNNHD to my "News" Channel Collection. Thanks!
The default categories is unrelated to the collections. They are dynamic filters that show the channels that have shows playing presently that are in the category, like if a movie is playing, then that channel is in the Movies category. You can have one or the other, but not both. You'll need to curate your own lists of channels for your collections.