Emulator

I can't reproduce this issue either. Loaded Mega Man 3 (VC) in PAL60, loaded Red Steel and shut down, then loaded Mega Man 3 (VC) in PAL again and it was still PAL60.

Try Wii Sport Resort USA

Ok, found out that revision responsible for this is 5.0-775 PR 4244 https://github.com/dolphin-emu/dolphin/pull/4244
5.0-767 works fine

Able to confirm this on 5.0-999, started with PAL60 enabled.

1. Loaded Donkey Kong Returns (USA) then quit
2. Opened Dolphin, can confirm setting is still off

Loading a PAL game works as expected with the setting remaining off after stopping emulation and restarting Dolphin.

More testing wasn't really needed since the issue was already accepted, but anyway…

Does PR 4319 fix this issue?

Is there a build of PR 4319 to download in order to test it?

Yes, http://dl.dolphin-emu.org/prs/pr-4319-dolphin-latest-x64.7z

Yes, PR 4319 seems to fix this issue

P.S. I've noticed that in the latest Dolphin dev builds "Enable Idle Skipping" option has been removed from the GUI (Options/Configure.../General)...was that intentional or not?

Yes, it is. And unrelated to this PR or 4319.

Something very strange is going on here, PR4319 fixes the two issues (or at least the build that I downloaded here did), instead 5.0-1042 doesn't fix anything for me...is it the same code?

Yes, it's the same code. It is however possible that the code is different in the PR now compared to when you downloaded it earlier. Can you try re-downloading the PR using build same link as before?

Make sure you are really using the latest build and not something else; one tester got fooled by Windows 10 not copying the build over :)

Otherwise, I just tested master and both issues are definitely fixed here.

I've just downloaded 5.0-1043 that has the same problem: every changes that I do in Options/Configure.../Wii seems to get saved (because when you re-enter the menu everything seems ok), but then when you close Dolphin and restart it, they get back as before (do not get saved at exit)

I've re-downloaded the (new) PR4319 from the link above and in fact it is broken like 5.0-1042 (the old PR4319 instead fixed the problem)

The old working fine PR4319 is called "5.0-1002 dirty" and the new one (broken) "5.0-1024 dirty"

That's a different "issue", which is caused by the fact that some settings are only actually saved when you start a game. So if you change some Wii settings, then close Dolphin without starting a game, they won't be used. I agree that this is a bit confusing, so the previous behaviour should be back in PR 4332.