I have exactly the same problem and, unfortunately, it appears to be a camera design flaw. In my case, the problem was becoming worse and worse. In daylight I could not take any single good picture in the auto mode. In manual mode, after several shots (more than 50) it appears that the problem disappears and the camera starts to work fine again. The flash mode and low light shots suffer less of that problem.
The movie mode works fine, so it is really difficult to guess where the problem is (It is no the lens, the zoom, the processor, the memory or the battery).
So the problem is driving me crazy (taking 100 pictures only to get the camera to work is not very nice), and I sent the camera for checking at the Fuji representative, but I'm afraid the camera is finished (actually I bought a Canon A510 which, while not having all the things of the e550, works fine).
It is so annoying that a company like Fuji offers a product with so bad quality control.