Apps moving from folder after update

Long time question really.. why do some apps jump out of their folder after an updat and others dont? is it something i can stop or is it an app thing or something else?

Well I feel like a real idiot because I just realized my problem is that Applications was no longer checked in my Preferences to Show. For some reason the update unchecked it, plus it wants to run the Setup every time I start now.
But at least my Apps are there.
I do have the manual, btw. Thanks.

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Apps moving from folder after update

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