Keyword your files so that they are all named keyword.png (or .jpg or .gif) then run the upl.bat file and log into your account.
There is DEFINITELY something up with uploading icons in general. It took me two tries to get all the icons uploaded. The first time it SAID it was uploading all of them, but then when I checked the first five and last five had, but the middle nine hadn't. So I deleted those from the folder and tried again.
Basically, just have all your icons in the same folder as those four files from the zip file, and go. Ping me on email or Twitter if you need help!
I ran this on Win7 just now to add more icons to Ade's journal, and didn't have to change any settings.