I just ran across this issue when upgrading to subsonic 4.5 (which appears to include an upgrade from JWplayer 5.4 to 5.6). This is how I fixed it.
I'm running tomcat 6 on centos 6, so your paths may vary. I did the normal upgrade process I always have of dropping the new war file in /var/lib/tomcat6/webapps and deleting the old deployed subsonic directory under that path. Unfortunately, JWplayer disappeared in firefox and was a white box in chrome (with the text "Movie not loaded" if you right-click on it). I ended up finding some cached files from the 4.4 install under the following path:
/var/cache/tomcat6/work/Catalina/localhost/subsonic
Deleted that directory, restarted tomcat, and JWplayer has returned

Hope this helps someone else.