Congratulations this is officialy the weirdest bug report i ever saw! I did indeed find a very strange behavoir, but a very differnt one then what u discribed:
When u select a single file within an expanded collection and using Ctrl+A Alt.binz does not simply select all files within that collection but all files within all collections. If you then try to split the collection either by right click menue, shortcut or toolbar button it does the oposite and joins all collection into the first collection in the queue...
Haha, I feel honored.
I've got a couple of friends in school that also program (smaller things but still), and they always hand it over to me for bug testing because I always give the most idiot input you can think of to a program guaranteed to make it crash one way or another. One time I was talking about a method one of their programs were using, and I found a bug in it without even touching the program at all (nor looking at the code).
Well it didn't show that the collections were actually selected, so I assumed it were only the files inside that collection, kinda confusing. But yes indeed, after your message I checked my first collection (which was on Pause because I want to download it later) and indeed all the files are in there. Thanks for that message, else I would have downloaded allot of unnecessary stuff.
But I can see where the problem comes from, if you try to split everything in a collection from a collection, it creates a new one as you described, deletes the empty collection, bundling all the files you just split inside the new collection with the same name.
It now does exactly the same, but with multiple collections rather than 1 only. So it actually functioning as it should, causing this wierd behavior.
But I don't see this as a welcome result of that operation, so perhaps a prevention might still be build in anyway.