For future reference for anyone who may need it the solution was to change following on my setup (kudos goes to Danny who got my brain suggested looking in the ACD direction).
On NuPoint;
Remove the Fax Group from the Voicemail Line so they are dedicated, one for voice and one and one for faxing.
Apply the configuration and wait for services to restart.
On the MXE;
Remove the fax numbers from speed dial which were originally pushing the fax numbers to the Hunt Group for NuPoint VM.
Have a separate HG entry for the now Fax Specific line group that points to NuPoint Ports specific to that group.
Create an ACD Agent ID and ACD Skills Group with the ACD Agent ID as a member.
In MultiSet Line Keys, go to a really high numbered button key on the users voice DID number and set that to Single Line, No Ring and the extn number of the fax for the user.
Create a new Call Rerouting Always Alternative and have that rerouting to the new HG for NuPoint Fax specific line group.
In Call Rerouting, set Call Day, Night1 and Night2 to the new CRAA you just created.