Ah, ok, that makes sense, I guess what I did would interfere with the location of the .rel files in memory.
All I did was tack the .bin to the end of the .dol file, and told it to be loaded at 0x80001800 in memoy... so I assume the loader.bin would have still been in the same location as it would normally be.
And yeah, I saw those files in the game dump, but did not look at them. And that makes sense, it does sound like a huge hassle.
And thanks for the help Treeki, I did not exactly expect that anyone would actually help give any info on this
EDIT:
UPDATE:
I moved the Loader.bin ove the top of those bluetooth error messages, edited the Loader.bin to account for the hardcoded offsets, and corrected the pointer to inject the loader from the new address.
And... same results as my original method... using Alt. Dol on original NSMBW disc loads the Loader after healthscreen, throwing Newer error screen, just as expected. Doing the same thing on my Newer .iso yeilds the same results as before, loads up fine, until trying to load world map.
Also, looks like I was incorrect about the title screen alternating, it just loads the same "default" jungle one (based on original title) every time...
So, looks like there is no difference in how I run the Loader.bin atm... I guess I would have had to packed the partition wrong?
But what I do not understand, is that, the titlescreen is actually supposed to alternate between different ones, right?