In that case, I'd try downloading VBA again, and run the ROM through it without modifying any settings. If that doesn't work, try a slightly older release (all of which can be found on VBA's SourceForge page) and see what happens. But since the game only crashes when entering a Pokemon Center, this tells me you may have bad sourced ROMs, which can be remedied by finding a better source or by ripping them yourself, to be sure you have clean backups.