You should run the same version of Emplode as is on your player. Doing otherwise causes Bad Things.

Actually, running the exact same emplode as the player is not required, as long as they both speak the same 2.0 protocol. The b11 player CAN talk to the b13 emplode and vice-versa.

There are bugs fixed in Emplode beta 13, but they are independent of the player communication, as far as I know. For example, the beta 11 bug that doubles your Visuals Favorites list with each synch doesn't have anything to do with which version of the player software you're running.