Can you run EmulationStation with debug logging and upload the log ? Exit ES, then run it with emulationstation --debug, reproduce the issue and then post the log file on pastebin.com.
The log file is in $HOME/.emulationstation/es_log.txt.
I've tried the steps you mention in reproducing the error, but as far as I see omxplayer stops once the screensaver is stopped.
Do you have any additional configurations in ES - namely any external scripts tied to the ES Scripting API ?