I think the issue is that your EB8's don't know about the controller. Each EB8 once initially registered with the base module, has a sort of serial number so it knows who its Momma is. For some reason, yours don't.
The way to fix this is to clear the memory of the EB8's, then re-introduce them back to the base module one at a time, in the order you want them numbered. As Todd points out, when you do this you will also lose your programming so it's important to save it first. First you delete the EB8's from the base module through the Module Setup screen. That clears them from the base but doesn't get the EB8 memory cleared.
You clear their memory via the display module System - Init Memory - Init Aquabus Dev. Then you unplug them, then plug them back in one by one in the order you want them numbered.
All this is not without risk however. Once you do a lobotomy to your controller, anything can happen when you restart it. If you don't feel completely comfortable with this, then reach out to Neptune. They should be able to walk you through the process.