Remote Buddy tracks Behaviours by their identifier, not their filename.

So what did likely happen in your case is that both of your Behaviours 
share the same identifier. You can find that identifier in BCK > 
Behaviour Factory > Specifications and Metadata > Behaviour Bundle 
Metadata > Identifier.

Please make sure your two Behaviours have different identifiers. That 
way Remote Buddy can tell them apart and should show both of your 
Behaviours.

Extra Tip: 
By dragging an application directly onto the list in BCK > Behaviour 
Factory, Remote Buddy fills out all fields for your new Behaviour 
correctly and also makes sure that the identifier for your new 
Behaviour is unique to that application and isn't shared across 
multiple Behaviours.

Best regards, 
Felix Schwarz