Ok. Quick update. Managed to have another go this morning. I took a couple of mm off the shaft. It is now definitely shorter than the original.
Refitted again. Lightly tightened bolts and checked the hub still turned ok by hand without any binding. All good.
But as I progressively tightened the bolts up it got stiffer and stiffer until it fully locked up the axle on that side.
Repeated procedure on the other side. The same result.
Put the old ones back on again and followed the same procedure as above - still good - no binding or tightening up issues.
Properly stumped!
Are the flanges the same thickness, if they are thinner they will pull shaft in further. Or I recall someone having a problem with the bolts being slightly too long for the flange and catching at the back, try fitting bolts with a temporary washer to see if it cures it. Or did I dream that.