Will all games ever work 100% on internal or external only?

I'm curious to know, is there any development in figuring out why some games only work 100% on either internal or external? I.e. for example GTA IV just wont work completely on latest version unless you boot it off external.

Is this all still a mystery or can someone enlighten me?

it all depends on the eboot,if thew game eboot has been edited it will only play of where is specified in the eboot

GTA IV works on internal in the original version though. It just stops working after you update to 1.06.

How can you edit the EBOOT?