I have some minor non-working thing:
Do you have similar issues with Mac&Mouse ?
I found one mouse (cheap Hama), which acts like this on my setups too. It doesn't work at boot if connected directly to the machine, but it works if connected via a hub (or replugged after the boot).
I mostly have Logitech mice otherwise and never had this kind of problems with them.
But you could try with a hub, if you want to use these mice.
I also reported this to the MorphOS team, so hopefully they can figure out something.
Workaround is simple - I tried four cheap mouses and two of them have same issue, two were OK. So I changed the mouse.
But anyway, all four works after restart under OSX and Linux.
AmigaOS: Micro A1-C, AmigaOne XE, Pegasos II, Sam440ep, Sam440ep-flex, AmigaOneX1000
MorphOS: Efika 5200b, Pegasos I, Pegasos II, Powerbook G4, Mac Mini, iMac G5, Powermac G5 Quad