Rate limiting happens by delaying, then dropping packets. You can not push 200Mbps of traffic through a 50Mbps pipe. Some will have to fall off outside the pipe and end up on the floor. The packets on the floor are "dropped" packets.
You are using the "default" or "default-small" queue type. Those run out of buffers pretty early in the throughput smoothing by delaying packets phase. When they run out of buffer space, they drop packets. If you are seeing excessive packet loss with 25 - 40 Mbps running through your 50Mbps queue, this is probably the problem.
You can increase the buffer size or switch the "default-small" and/or "default" queue types from using pfifo to sfq. The defaults are not good defaults in the days of >10Mbps network links.
If there is more than 50Mbps of traffic attempting to go through your 50Mbps queue, you *will* have packet loss. Switching to SFQ may help to keep any one connection from being penalized too heavily while other connections get all they want.
Please read and understand http://wiki.mikrotik.com/wiki/Manual:Queue