re: Are you running PHP under FastCGI?
Yes.
We have since upgraded to php 5.5, use disks with faster access and use Opcache. This seems to have solved our problem, rock solid since then, cant tell if it was just the php upgrade or a combo of the 3 things as we did it all within a slow 2 week period. Php 5.5 seems to be another step in the right direction for windows/php on moodle.
in hindsight I still think LAMP would be a better long term move as there is not enough of a support/developer community with Moodle/WIMP. I've been exploring MUC caching and most documentation/support is for Apache/Linux.