Yes the bug is this line: bearing_height = min(65, 2.8 * bearing_length); in x_end.scad.
The intention was to keep it at 65, (same as Prusa) for 8mm and 10mm rods but make it smaller for 6mm Huxley version.
Here is a backwards compatible fix (I think):
shelf_thickness = 2;
shelf_clearance = 0.5;
bearing_height = max( min(65, 2.8 * bearing_length), 2 * (bearing_length + shelf_clearance) + 3 * shelf_thickness);
Note that will make your rods and sheets bigger. Sorry about that.
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