It really depends on how many objects you have in your ARS system. What is happening during that 'hang' time, is arsdoc is loading all of the objects into hashes in memory (yuppers... watch your memory usage on that machine when running arsdoc... quite scary!). Once it has them all loaded, it starts processing them. It begins with Active Links, and then moves on to other objects.
I normally kick off the process on a separate machine and then go do some other work. I haven't timed it yet for our system, but it does take a while!
I would try just letting it go. If it's not crashing (error messages, etc) then it's working...

Let us know if you get it going!