This is a VBA problem. It also distorts the sound terribly. I've tried No$GBA which worked fine, though other GBA emulators may work as well. (The VBA has problems with the unpatched Japanese ROM as well, by the way, so it's not a problem of the patch.)
Anyway, thanks for your amazing work, magicalpatcher! A news post on the website for more exposure would be great. Siliconera already posted news of the translation.
Magical Vacation really does look incredible; surely one of the most beautiful GBA games. Will play more next week. So happy we finally get to play this game in English!