Books don't actually "enter" collections. rather they have the label of also belonging to that collection of books have the label "Whatever". IIRC
So this is a calibre import-export question really. Looks like the tags are getting mushed together. I have never used this for/with Calibre export but recall something about either custom fields being missing, or being needed to be setup. Sorry that is all I can dredge. I'm not even 100% about that...
I recall Niluje and Ixtab chatting about this (or a very similar) subject a while ago, perhaps they will have something actually helpful to add.