Reply to Instant Gratification and Midi Fighter Classic - Midi notes?

Hey All,
I'm looking to move my effects between the units so I can utilise the the layout and the effects knobs better with the Instant Gratification mapping.
I understand the basics of what to do but the problem I'm having is the MIDI notes listed for example 'Deck A' are not what the MIDI Fighter is sending for Deck A!
A further detailed example is as follows:

To activate 'Filter:92 LFO'

(as per the controller manager)
Effect 2 On - In - FX Unit 3 - Hold - Ch03.Note.A#2

(actual MIDI message being sent from MIDI Fighter on Deck A for that effect)
Ch03.Note.A#1

Now, somehow these two are connected and working! This completely loses me as surely the controller manager must match the received key unless there is some weird converting going on?
Can somebody shed some light so I can get into the MIDI routing? I'd love to get more into it and I also have a second MIDI Fighter Classic I'd like to make use of.

Any explanation of whats going on here would be great as I'm stuck in thick mud and going nowhere...

(Oh by the way, this is for all decks and effects! Its as if they're all shifted up one category!)