Confirmed that this is caused by something in the recoloring code. If I get rid of the recoloring effect on default:owa_XXXX, it no longer has this bug. (Of course, it doesn't recolor either without that line.) I further tried adding this recoloring effect to a different object (specifically, default:flag_blue) and sure enough, it started exhibiting the bug too.
Here's the result of various arrangements, and how they come out. All of them function correctly; the bug is purely visual.
For reference - the first set of directions (without the "2"), the opposite direction is made with a single flip or invert (as applicable). The ones at a 90 degree offset are made with a single rotation from the original state, then a single flip / invert for the opposite direction. Then, the ones on the right are made by copying the ones on the left, and flipping / inverting them - whichever one would not affect physics.
Of particular interest, is that some of them do actually come out correctly - or come out as a different wrong orientation. In all cases though, the alternate orientations don't get recolored.