I think MPT should work with base56, but if you fixed your issue by editing the slot to 250 (base57) that's good.
maybe your slot249 is not correctly installed? (but usually it unsync the wiimote if not correctly installed. Maybe there are different symptom of an incorrect installation)
To play games with multi dols (menu and multiple games to reload, like Metroid, sam & max, ssx blur, red steel, and any motion+ games ), you need d2x v7 or newer and set "block IOS reload" to Auto (or ON).
d2x v8 is the best choice.
@GreyWolf :
I'm not sure to understand your javascript implemention.
are you compiling ecma parsing and interpretation inside the loader?
where would it be used? what could be done with it? adding menus and options? would be great! but will need parsing in all possible location of the loader to add a proper plugin system (like firefox xul where you can add/edit content of each menus, linked to javascript)
Maybe it will be too much changes, we could reserve it for next major version (4.x)
what I wanted to do for plugins is a menu where you can list all installed plugins (or add new ones directly from the loader, to generate the ini/xml)
for each listed or created plugin, you could edit the content : rom path, dol path, etc. directly from the loader.
that was what I wanted to do AFTER the overall GUI modification (USBGX 4.x roadmap)