Remember it is a constant mesh box so you are turning a lot of gears with cold oil on them, new oil seals as well? it will drag much more in any neutral except between 1st and 2nd, (when only the output dog clutch is engaged) and it has yet to settle in.
Had a similar thing with my gearbox, it did not turn very freely at first, it dragged slightly in one place like an oval brake drum. I was worried about this as I had put some bearing retainer in to stop the bearing outers turning, and thought this might have set too quickly before I'd tightened the box together and squeezed a bearing.
But a bearing would be tight all the time, not intermittent, so it must have been a miss matched gear or spline, it would only have to be a couple of thou or so out.
I drilled a flat bar to fit the flanges with a long bolt through the end and used this to turn the gearbox, from both ends, gave it a vigorous wizz up every time I passed it. it freed up a lot after a while doing that, but was not absolutely perfect, me being too picky I suspect.
When I first drove it I imagined that I could hear this but it soon went away and the box is very quiet, or else I've gone completely deaf!