Intonation set but first fret way out of tune

[Lemonpoet]

I have finished the build on a IB-1 and found that I cannot tune it.

The intonation has been set but when the first fret is held down eg b string first fret is nearly c#. E and E are nearly f#,
I have removed the shim under the nut thinking the nut was to high, this helped a bit. I've also adjusted the truss rod so that the strings are just not buzzing.

I have placed a block of wood on the floyd rose so it cannot move, after I get it tuned then I will work on tuning with the floyd rose released.

Does anyone have an idea how I proceed? Has anyone else built one that can be tuned?
Is it possible the nut should be moved away?

Is it possible the nut is in the wrong location? Other ideas, maybe shim the neck joint to flatten the neck to the body
it





Cheers

Geoff