I wanted to throw this out if any other folks experience this later on. At Digg we've been using the BufferedTransport + C extension of Thrift in PHP. Every so often, we will see spikes in latency increases on RPC calls that we know have acceptable response times (<200ms). This seems to happen based on how much data is being sent back over the wire. This is more of a PHP problem, but can be corrected in Thrift's PHP library for folks who don't want to upgrade PHP. I am still waiting to see if it's corrected in later versions (we use 5.2.9).
Replacing the fread statements in TSocket.php with stream_socket_recvfrom correct this behavior so that calls do not wait until they hit the recv timeout.