Test 1: 4.3u Wii, softmodded using SSBB Exploit. Everything went fine, used r416 WiiFlow, but it would occasionally freeze, give errors, and do strange things after coming back to the WiiFlow Menu from a game. It's my Wii so i didn't pay much attention to it. few extra seconds getting to the menu didn't hurt me.
Test 2: 4.1 Wii, was already softmodded, so i just upated the IOS and installed the rest of the WADs mentioned in the guide. It never froze, no problems, no strange things.
So I concluded that by updated the IOS from the guide, it somehow affected it. SO, i updated the IOS on my own Wii, that was originall 4.3u. As you know the guide mentions there's no need to update them. But from today, I found out it doesn't hurt to at least run the update for the IOS even if on 4.3u already.
Hope this information helps others.