I've had similar issues at times messing with VSTs and this program: MidiPipe by Subtlesoft (Mac only) solves everything for me. I can't link it because the forum censors it but a quick google search will show the site. This program basically unlocks your Midi Controller and allows you to have full control over what messages you send.
At the very least, it will show you what Midi Messages you are sending through the A List plugin.
For a quick tutorial, just put a Midi In at top and a Midi Out at bottom. Set the Midi In to be one of the recognized Midi devices and set the Midi Out to be one of the MidiPipe Output # (1-8) for one of your controllers.
Now put the A List plugin in between the Midi In and Midi Out and click it and watch what messages you are sending. You can then put a Key Mapper plugin above the A List and choose for all the notes to be mapped to a specific channel or a certain group of notes to be mapped to a specific channel. Then you can watch the A List to see what happens.
Pretty much when all else fails with my Midi Controller to DAW scenario I just hook up the MidiPipe and "force" the issue in a way.
Quick tip: you can open up Terminal and you can execute this command >>>>> open -n /Applications/MidiPipe.app
This will open a new instance of MidiPipe where you can plug into it as many Midi Controllers as you want. With MidiPipe you can use the Key Mapper plugin to make a single controller send on multiple channels, so this may not be necessary depending on what you need.