The temporary table should be empty when you have finished with the spidering process. Sometimes the process hangs for no good reason, and I have yet to figure out why. I've had that happen a couple of times, but when I started over, it worked like a charm. Go figure.
You might try emptying the phpDig tables and starting over. Before you re-index though, make sure the value for LIMIT_DAYS is set to zero so you'll be able to do that.
If you still have problems, let us know. We'll be glad to help.