Ok, so it appears I've found the solution to my problem. When the CPU affinity is set to anything other than "<All Processors>" the game stutters... however the setting in CnCNet which says "Force single CPU affinity" doesn't have any effect, the game loads with CPU 0 only by default, no matter what. This means I have to manually set the CPU affinity to use all cores manually every time I launch the game.
I suppose this is something to be looked into for a future update, maybe.
But for now I have a solution; an inconvenient solution, but a solution nonetheless.
Thanks for your help!