We ordered a dozen red SB-50s and received a dozen grey ones. When we went to plug them in they didn't fit. We just milled down the connector where there was interference and red plugs into grey just fine now. The contacts are what holds them together anyway. I'm not positive about other colors, but contact position should be the same on all of them. You can see our setup
here.
Otherwise, what about organizing your wiring a little better so it is easier to trace? Or labeling your ports on the charger and then labeling you battery positions? In the above linked picture, we had a hard time figuring out how we wanted to organize things, but ended up with a visual layout. The batteries are arranged top to bottom by number and on the charger they go from the middle to the out side by position. You can see how 9 and 10 are not lit up on the charger because they aren't in the cart. If we unplugged battery 1 on the bottom left it would turn the light off on the far left side of the charger.