I worked it out (sort of).
After trying all your tips, the reader still did not work in any way.
Almost ready to throw it out of the window, I tried to insert an old USB 2 Hub between de HP microserver and smartreader.
Immediately, the reader started working, exactly as before on 5.2.
I tried to remove the hub and immediately it stopped working again. I also tried different BIOS settings regarding USB, bot none worked.
Lsusb only shows the device when connected through the hub.
So the only way to get the smargo working for now is to use the old (Sweex) USB 2.0 Hub. I am okay with that for now, but if possible I would like to connect the reader directly.