I'm having the same problem. I've been using Links 2.0 problem free for over a year up until now. When I do a build, it only builds up to a specific category and then stops. I've checked to ensure I have enough server space, and I've tried deleting the links generated HTML pages and rebuilding (which it does, up to a certain point and then stops). The site has just under 1000 links now.

Ack! Can anyone provide any insight?!!

Thanks in advance!