Yikes... I don't know... I would check all the settings, and if everything looked right, I would reset to factory default. If you don't know how to do that, download the manual and it tells you... Or let me know and I'll be more specific.
I had that problem with S2 too... and like you it was a battery low issue (CR123's). But my S2 finally kinda died recently when I was rear ended in a car accident. DANG PEOPLE - Don't they know to not hit you - you are carrying a camera
Anyway... Camera was in padded case, but apparently it still got jostled around. It worked fine for about 50 frames, then it started giving black frames (which I never had before). IF I shut it off for a while, and turned it back on it'd work for a few frames, then back to black... If I changed settings, or went to manual, it would work for a few then to black, then I could switch to AP, shoot off a few, etc.... Slowly over the course of 2 days, it went totally blah... Then it worked again after setting off for a few days, etc. I'm still trying to save up the money to send it back into fuji for repair... if they will even still repair the S2's. I LOVED that camera so I'm praying!!!
I bought the S5 in essence to replace my dying S2... So... We will see if it was a smart move or not
Umm... What I am thinking though is that it is set to a very slow shutter speed...
I'm hoping that's all it is
I am thinking with the S3, it works differently than the S2 did for shutter lock up (like for cleaning CCD)... if I remember right.
If all else fails, you can send it to fuji, and they will tell you the cost BEFORE they repair it, and they charge a flat rate to just look at it (off hand I'm thinking somewhere around $50, but I could be wrong on that too)...
Anyway, I have S2 (which is dying), S3, & S5, so let me know if I can try and help you more.
And the more I think about it, the more I think you should claim it damaged... Did they send it UPS or fedex with insurance?! Yikes, I'd hate to be in that mess.
Also... you know... you should have considered just diving into the S5, they are low priced right now... I think I got mine for like $1500...And if you love the DR on S3... Look out the S5 offers ISO 3200... which is too cool. In P mode, I was able to take a well exposed shot in almost complete dark without flash (and the lens on it was a 3.5-6.5)... I can't wait to try it out at a wedding.