I can't guess the connections but often when Samsung updates firmware (they can do so automatically and without notice) a setting is lost. You need to go over all settings as if it came out of the box or just call Samsung (1800SAMSUNG or www.samsung.com) to see if they know which settings to check.
I have had a Samsung HT-F5500W BluRay surround sound system hooked up to my Samsung U60F7100AF 60 inch tv since I bought it with no issues. It was working as of this time yesterday. Today when I turned on the tv the blu ray did not turn on with it. I manually turned on the blu ray and it does play sound. I have tried a DVD and get sound. What could be the issue? All firmware is up to date and no connections have been changed