I have been doing a number of tests and concluded that there is something wrong with the crawling. Depending on where I make it start, I get 1 page or a few pages, but always only a fraction of the total pages of the site.
My site is at:
[external links are visible to admins only]
I have tried the online version and it gets to the 500 limit without problems starting at the root.
Otherwise the program seems to be installed correctly and all file permissions are fine.