If you're using exactly the same version and same settings, then they should run the same way. MAME32 is nothing but a GUI on top of the official MAME. They don't change the core at all. There are minor differences tho, like different defaults, but nothing which will make a game magically faster or slower, once the setting is changed.
You must have overlooked a setting. What you describe is probably the frameskip. In one the default frameskip is auto, in the other is 0. With games like that, you want frameskip 0. Also keep an eye on the sleep and RTDSC settings.