@T3kNi9e - There are some VC games where you're supposed to be able to use the remote sideways as a controller, it usually specifies in the description before you download.
@skinteedee - Have you tried re-synchonizing the remotes? I forget how to un-synch them (you should do that first, probably; Google it), but you synch them by pressing the red button near the SD card slot and then the red button near the batteries in the back. Also, try a different remote to make sure it isn't a problem with that remote, and if you have anything connected to the remote, unplug them. Lastly, maybe try switching batteries too? :P