I have experienced the same issue, but seems to managed to get this resolved.
I have about 90+ sites and also go the same geocoding issue.
I have increased the time limitations on the file as per previous comment. And this still dit not work
I did use co-ordinates and this also did not work
My last change was to change"Drawmaplinks" to false.
This can be found under: Infrastructure -networks- configuration properties
Now i can see all my sites. It still does take a while before displaying all of them.
It been running for 30 minutes without issues. So hold thumbs this is a solution we all can use.