dstiles - 8:50 pm on Aug 13, 2011 (gmt 0)
1script - you say one of your DNS servers failed. Could that be a lot (not all) of the trouble?
If google failed to route to your working DNS server and couldn't find an alternative it could have returned errors; whereas, because YOU could get your site via that DNS (probably cached locally by you) you considered it live. As, quite probably, did a lot of other people who could route through that DNS server.
This would particularly explain why your logs have no entries for certain times that google claims you had errors.
It would also be worth checking that there are no problems with your working DNS server (and presumably, now, your newly working secondary one).
In the UK I use intodns.com to check DNS faults. It would be worth finding US-based tracers as well.