Well, we found the issue! I started to look at the WMT crawl info and there were a bunch of network unreachable errors. Here is what happened: our site being

Well, we found the issue! I started to look at the WMT crawl info and there were a bunch of network unreachable errors. Here is what happened: our site being PR6/7, we started getting a lot of scans for exploits. Some of them over and over. A few months ago I wrote a rule-based procedure to automatically block these IPs at the firewall level. Well, someone had tricked Googlebot into searching our site by using a "break in" URL, so Googlebot fell trap to that and got blocked. Interestingly, most of the access to our site from Google were from one IP and it was blocked for a little while. In the end, since the "admin" site was a copy of the main site, it effectively acted as the backup! We've taken steps in the rules to not block Googlebot :)