When you start RLM two processes are spawned: the RLM process and the lightmap process. If you shutdown the license server by killing just the RLM process, the lightmap process will continue to run and a subsequent restart of the license server will fail saying:
(rlm) Port 5053 in use, waiting...
It is recommended that you shutdown the lightmap isv process first, followed by the RLM process. You can use rlmutil to do this:
./rlmutil rlmdown lightmap
./rlmutil rlmdown RLM
If you do find yourself struggling with Port 5053 in use, the simplest solution is to restart your computer. That will kill this process as well as all other running processes. If shutting down the server would make you very unpopular in the office, ask your systems administrator to kill the individual rlm process then start RLM again.