My understanding is that the DS rumble pak rumbles any time the GBA bus is accessed. If that's the case, it would not be possible to both run a GBA game and use the rumble at the same time.
I think that is how it works, because if you use GBA ExpLoader to enable rumble then start GBA ExpLoader again, it says "Slot 2 expansion pack not found" and shuts down. I'm guessing that once the 3-in-1 is set to rumble mode it can only be reset by turning the power off.