First, please, make sure that Hide Movie Controls option (Window -> Hide Movie Controls) is not enabled in main menu. If it is enabled, please, click Show Movie Controls (Window -> Show Movie Controls).
If Movie Controls are still not displayed, please, delete the following file which contains preferences for SWF & FLV Player and relaunch SWF & FLV Player to restore default settings: ~/Library/Preferences/com.eltima.SWFMoviePlayer.plist
The issue should not persist any more.
Please, also note, that when you delete the above file all of your preferences for SWF & FLV Player will be set to default.