What about having a pokemon with a hacked move in the PC or having the Game Time Maxed out at 999:59? Neither of those affect the RNG either, right?
I'll post my results that I find tomorrow after I get off work. Hopefully that will help. And thanks in advance (pun totally not intended) whether or not what's going wrong is revealed.
Nothing has an effect. The seeding function is skipped entirely due to a mistake. The default value is 0 (that is the case in R/S btw, except the seeding function there is called at the 6th frame or so to overwrite it). The only time the seeding function is called in Emerald is when starting a new game.