Thanks to those of you that contacted Cloudflare directly and sent your traceroutes (and cc-ed me). It was helpful in narrowing down the potential problem areas. A couple of fixes are filtering through right now. The big one we hope was the cause was our ISP and the network connections between us and certain points in CloudFlare's network. It definitely had reproducible problems between us and points out of San Jose and Chicago (the two tested as baseline).
More updates as I get them.
N54 / Steven Roussey / My Weblog
/ Follow on Twitter