I have been facing almost similar throughput issue with MX450 release version 16.16 in 2 sites that is geographically separated. This started since July13th and we don't see any kind of packet loss or jitter in the path, but the throughput is very less around 100Mbps(1Gbps line speed)
But when we check the dashboard throughput , it is around 600Mbps. More over when we use a proxy , the speed is decreasing from 100Mbps to 1 Mbps. Anyone facing the similar issues?