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Hey, just wanted to bump this thread since I too have the same problem since a few months back. I can't answer your question about different websites as i use mangafox for 95% of my mangas, though with that said, all the mangas that are merged together are, as expected, from mangafox.
I'm using the beta channel, v. 1.5.4.1 but have had this problem since at least last summer.
Mangas usually end up in the "collection" when I've read them for a while, but I've also had some mangas get directly added to it. When they are in the collection they still update correctly but never notify you about new chapters.
Initially I thought the problem lied in some special sign in the mangas name making it unreadable to AMR (notice that no manga have a name in the collection) but I haven't been able to see any re-occuring letter or sign in their names.
Finally I think it's worth mentioning that I have been able to retrieve some mangas from the collection simply by removing it from the list, restarting chrome (prbly not necessary but oh well), and then simply adding it again. Unfortunately this doesn't always work, some jump back to the collection immediately, some after a while, and well, some stay corrected.
Image! Notice the small "minus" sign in the top left, these are all mangas in my "collection-slot".
Please do tell me if there's anything else you want to know, I'm happy to help
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