I don't have chemical skills to explain this difference in crystal aspect but I performed 2 or three Rue extractions, which gave the same results. At first, Manske gave nice and long crystals and the last ones gave a sort of gelly, made of very little crystals. Nevertheless, the final product, after 5 Manske, was perfectly fine, under the form of FB harmine and harmaline.
So, I'm not sure you made a mistake... Or we both made it.