Flying is not enabled when it is enabled

I made a command block teleporter, and when I teleport, I'm dropped through the floor temporarily and reappear where I should have landed (this is usual). I'm then kicked because flying is not enabled on this server. Assuming poor performance of internet or something, I just enabled flying is the server.properties file as a quick fix, but I continued to get kicked and now I can't do anything. Even restarted the server.