Thanks again, the amount of confusion is actually getting smaller...
See attached (if I'm able this time to attach an image...) example of how FLIRT (and most FSL utilities) are using rotations.
They are actually rotating the image about the upper right corner (and many other operations are referenced to that corner too, like changing FOV in FSL).
So, for a proper -fsl_matvec (at least with FLIRT 5.4.2) the FLIRT transformation matrix would be as mentioned before
a b c d
e f -g -h
i -j l -m
0 0 0 1
plus a shift due to rotation around the upper right corner instead the center.
Wolfgang