Some more info.
On loading the save nanites go from the factory to the projector hologram and return green suggesting they completed their task but no blocks have any progress and the nanites will not return to the holograms until reloading the save again.
The factory it self says there are no projection targets.
The grid has both a projection and repair beacon and is like 10m away from the factory.
Docking the ship to the station sort of helps but it is extremely slow. EDIT: Sometimes the NCF is showing projector nanites getting stuck while docked
Debug doesn't show anything wrong.
I've tested in a world with just the nanites and projector plugin and same issue, sort of need both for my play through so hopefully there is some workaround

Last post, it seems its not to do with the projector at all, maybe my base is too big but scanning is taking like 2 hours and the facility just isn't doing anything, it's saying there are not enough components when the 100% are more than enough.
I see there is another thread talking about the slow scanning so I will post there instead.