First it looks like the bubble may not be centered
the same in all pictures.

Second the numbers and lines on the scale
may not be centered properly in the meter.
You can check this by making the rail level
on a flat surface. Use a stack of (razor blades
or something similar)under each end of the rail.
Adjust the number of blades on each side until
it is level. Once it is, turn the rail around and
see if the reading is the same. If it isn't you may
be able to take the thing apart and move the
numbers to where they belong.

If this checks out, do the same thing using the
wing clamp things to check the incidence of
a piece of window glass or flat metal. If it
is not the same both ways, you can file one
or both rail slots and shim them to hold the
rail in the proper position.

The final alternative is to always use the
incidence meter facing the same way.
The incidence angles are only important
in relation to other incidence angles, such
as top and bottom wing, or wing and tail.
If they are all wrong by the same amount
in the same direction, it is as good as right.

Jenny

ps Before you get your panties in a knot,
yes, thrust angle does relate to the incidence
angles, but it is usually a separate issue
more related to CG, weight, and speed
and drag. So, it is adjusted after the plane
is done and flying.

And no, the "incidence" of the fuselage
doesn't make that much difference.
Maybe a little, but mostly it is not enough
to warrant much attention.