After a few emails with the Flux support, it seems as though this is an issue they are very aware of and in the process of fixing. A feature which has been added in the new IRCAM tools allows you to force a certain number of ins and outs within the Flux plugin, which is then recognised by the DAW. This feature has been implemented on the windows build of the regular Flux plugins, but not yet on the Mac version. Flux did very kindly send me a Beta build of a Mac version which has this feature and I can confirm that it works, accepting all 8 channels from Reaper and allowing you to route them as normal in Flux. This update is due for release in January and will be a free downloadable update. Time to beat the UK VAT increase and get these bought!