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Do you use Gnome or KDE Plasma?
(sh.itjust.works)
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I imagine it's due to the default apps not being changed when you switch between the environments. For example it's probably still using GNOME's Files application in KDE instead of Dolphin (or maybe vice versa). You should still be able to manually launch the "correct" app in each case, but of course you'll have to know which is which. There's no actual problems created by having both installed, but most people don't because of this and other annoyances.