The message cl_FlushEntityPacket is what you get when you're experiencing a large packet loss (lag). If you wait, you might notice that all of the game entities disappear, and if you're lucky enough to re-sync with the server, appear again, possibly moving very quickly for a short period of time.
Basically, it means you're lagging pretty badly as a result of a connection problem. If this happens on one single server, it might be the server. If it frequently happens on every server you play on, it may be on your side.