I ran into a pretty unique situation with crawl rules and search. Here's what happened...
After lots of internal emails, banging my head against the desk and etc... i decided that it had to be simpler. Luckily i had server access and noticed that when i fully qualify urls ie stops sending an NTLM authentication ticket. You can get around this by adding the url to your intranet zone. I then went into the content source and noticed all the urls were fqdns. I then used the local names (took off the domain suffix) and voila everything works with the crawl rules. Why were the crawl rules causing the crawler not send the ntlm ticket or whatever else the issue was i have no idea. All i do know is nothing was in the event log and the trace log even on verbose. The long term solution will be to add the proper registry keys as detailed in this support request, http://support.microsoft.com/kb/303650/en-us.
Hope i saved someone some from a few days of headaches.