BUT! After two painful hours of making sure im not seeing things (im still not sure, though) i think ive figured it out.
Thus, with outrageously upscaled images (because i have issues), for your guilty viewing pleasure:
( WARNING: Sanity not guaranteed. Might contain pink elephants. )
1. Move the core away from its default position.
2. Create section09 and input these coordinates: x: 1100 y: 1020.
3. Make a screenshot:

(added grid lines as an overlay, they actually meet at 1099, 1019)
4. Flip it along x axis, then flip it along y axis.
5. Rotate it 180 degrees.
6. Make a screenshot:

7. Compare.
So it gets shifted 1 pixel to the right and 1 pixel down, no biggie...
But wait, theres more!
It actually doesn't get shifted. Its the point around which rotation/scaling/flipping happens which is the culprit. This leads to some retarded behavior.
Before retardation:




Notice the red dot? Its that point around which the whole sprite gets rotated. Its also the point of section coordinates.
After retardation:




\o/
This also applies to scaling.
Everytime you flip a section, this point gets shifted. And a pink elephant dies. How many more have to die?