You seem to be having more problems than anyone that is not stuck with a microSD to miniSD adapter (or a fake/bad miniSD) and that you are having issues with updating the loader is really not good- it points to issues with the miniSD cart.
Are the super mario titles named using 8:3 naming- that usually solves everything for those games until you want to try forcing through unlocks from the ereader stuff.
The others- the usually worked fine for me and if not then the SRAM patch of GBATA usually saw them working fine-
http://www.no-intro.org/tools.htm
I can not recall and I am in a bit of a rush so no looking up right now if those came with bad versions, intros and such, although for the most part that should not have troubled it, but I will say I always use clean versions of the games. On ninja 5 0 I probably used the other version (ninja cop) instead mind you.