Mixer assignments problem with Reason

We have Reason 4 wired into Logic 8.02 via rewire as many separate tracks but when we installed Groove Agent 3 the track input assignments all changed and some of Groove Agents had taken over. This can all be re-assigned manually (time consuming..) but then the same problem happened again when trying to use the file on other computers. Disabling Groove Agent in the audio units preferences did not help and even when loading files that have no use of Groove Agent the assignments are wrong.
Installing Novation's Automap for their Remote keyboards also caused a similar problem. When you look at the input assignment menu on a mixer track you can see that Groove Agent and Novation's Automap now have menus of selections that have installed themselves above the Reason assignments menu.
What's going on? We can't keep on reassigning all these inputs all the time, they should remember what they were set on and keep those settings surely? Puzzled...

OK incase any kind soul was about to try and come to my aid, I've worked around the problem by duplicating all the affected tracks, re-assigning the new tracks back to the reason instruments they originally corresponded to (deleting the automation in the process) and then moving the original midi info and automation across to the new tracks. Still puzzled as to why this happened in the first place. Any light that can be shed would be appreciated.
Ta

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