Then you should check your rival scripts, 'cause I hadn't problems due to me picking always the same starter, so I never realized that problem and had to do an extensive look through the script to notice there was a part of the script getting overwritten.
Usually rival scripts get long, so it's easy to get lost regarding offsets (I don't know if you are as stubborn as me about compressing the scripts as much as you can, you should, if you are using Emerald), run a deep scan there many times. If it wasn't something there, then, probably it was something on the starter script on Elm's Lab.
Anyway, the game has a normal ammount of bugs in my opinion. Just fix them for the next Beta (I don't think we need a .5 so early)