yes, looks really strange.
Just some ideas which I could imagine lead to such a problem:
(0) on any image or just some specific ones (maybe also test with some JPG as input).
(1) what is the size of the cropped area, is it damned small ?
(2) auto-levels ON ?
(3) any processing active (e.g. NN, WaveletDenoise, ...) ?
Some time ago I was playing a bit with Photivo ... and there I could see similar (or even more strange) efefcts in the histogram depending on the filters applied to the image.
OpenSuse 11.4 (32bit)