To make a long story short, we were basically not telling Steam that we were done with a Master Server Query and one of Steam's recent updates, we believe, started looking for a Query to be completed before it would allow another one(probably to reduce load when people click refresh 1000 times a second =)
Just a small glitch on our end that only became apparent when Steam changed their end, quick fix.
Please let us know if you continue to have this issue.