I am trying to run GenesisPrefs, but when I double click the Icon, nothing happens. No program comes up.
You should update your OS 3.9. This was fixed long ago and other serious bugs have been fixed, too.
http://www.haage-partner.de/download/AmigaOS/If you don't want to update, get the gendemo archive from Aminet and extract the MUI classes from it.
I have found out that if I transfer a single (large) file, it will transfer at a relatively high speed - but when transferring WHDLoad games folders it just gets stuck at very low speeds.
I cannot help with your network problems, but I wouldn't use the network to transfer such a huge amount of data at all. I would connect the HDD from one computer to the other computer temporarily and copy files directly from HDD to HDD.
Bye,
Thomas
