To confirm if your settings are the same after reselecting the device, can you save the configuration (by typing a name under "Profile" then clicking on Save), then close Dolphin, reopen Dolphin, reselect the device, then save the configuration under another name, then:
to check for differences.
Code:
diff --unified ~/.dolphin-emu/Config/Profiles/GCPad/*.inito check for differences.
