Combining two led strips with separate controllers
If the controller output parameters like brightness, speed of animation, color are not in sync between the two led strips then you need to reset both controllers to there initial states.

These kind of controllers store the previously set parameters in their memory and thus are able to start from the previously know state on each power cycle. You must have set different parameters for the two controllers before you combined the receiver sensor output. 
i.e. If brightness in one was set to 50 and in the other to 25, then since they have common receiver sensor now, on increasing brightness by 10, one will increase to 60 and the other to 35.  

To fix this sync problem you need to just keep lowering the brightness / speed of animation / the parameter not in sync, until the parameters become equal on both.