I'm just making an initial guess, but...
Most devices default to sending midi data on certain channels, and receiving on certain channels. Most allow these channels to be set/changed if you want to do something different.
Maybe your previous setup worked because things tied in with the defaults, or how you had things set. Now that you've changed one or more of the devices, things are slightly different. You need to keep checking the channel settings. You don't say how things are working exactly, but one thing that might be happening is that you are sending the right data on the right channels, but there may be some wrong data on other channels as well.
You need a chart. Consider ALL the devices as a complete system. List the 16 channels, and check what is sending on each channel, and what is receiving on that channel. If you send data on Ch 1, and two devices can receive on Ch 1, then both devices will respond to that data, like it or not.