Curious question :D

Ok so I modded my Wii a while back, it was 4.1 when 4.2 was well released, I have Call of Duty: Modern Warfare: Reflex, and it never asked me to update to 4.2. I modded my Wii (softmod, homebrew), and ever since it's asked me to update if I want to play Reflex through the disk channel. It's not really a problem for me as I just load the game through Gecko OS now, but I'm curious as to why it only asked me to update after the installation of Homebrew.

You messed with IOS didn't you? You downgraded or deleted an IOS that is on the disc, and now it wants to install it. It's safe to do so if you want, or you can use Priiloader or StartPatch to block disc updates in the System Menu.

Ah ok, that makes sense.