Beg to differ here. I’ve used two armatures on a mesh regularly by way of the Armature Modifier, since they can be stacked. Only one Armature can be a parent to a mesh, but influences on vertices can be shared by more than one Armature object.
Of course there are limitations, since balancing the influences is more complicated, and it probably won’t work properly in the BGE until they get it to see the Armature modifier, but it’s often a good solution to certain deformation problems. For example, I use two armatures in my Othello model/rigging, one for the body, neck and head motions, and one for just the facial stuff. The body-posing armature parents the face rig, which in turn parents a separate rig for just the eye motions, btw. There aren’t a lot of verts shared among the armatures, mainly in the head & neck, but it works OK nonetheless.
To the OP: make sure that the armature you want to paint weights to is that which has most recently been selected in Pose Mode. That should insure you get what you want. But in my experience as long as both armatures have been put into Pose Mode, I’ve been able to select bones from either in order to weight paint. In 2.49b or earlier that is, haven’t yet done this stuff in 2.5