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Barring a malfunction with your len's autofocusing mechanism, the problem that you're experiencing is likely due to the limitations of the camera's focusing / zoom range in Macro mode.
You didn't say what ranges you were shooting from but basically, in order to get proper focus, you must first make sure you're within the proper lens to subject distance for the macro mode that you've chosen.
There are two macro modeson the S5, Macro and Super Macro. Macro shooting is done only within the ranges of 3.9 inches to 1.6 feet from your subject. SuperMacro mode (which is entered into by simply pressing the Macro button for one second) will only focus within the ranges of 0 inches to 3.9 inches. So if you are in either of these modes and stray from their focusing ranges, your camera won't focus properly.
Another issue that you may be dealing with is the very limited zoom range in Macro/Super Macro Modes. The zoom is basically meant to be set toward the maximum wide angle end of the zoom range. There is a yellow indicator bar below the Zoom Bar in the viewfinder that indicates the Out-Of-Zoom range in which the zoom basically can't be used. As you may see, only the first 10% or so of the zoom range is useable.
It might be that you could possibly be wavering in and out of the two macro mode focusing ranges and/or zooming into the Out-Of-Range zone during your session. Either can cause a similar effect such as you are describing. It's hard to say without actually being there.
To test this out I would simply set my camera on a tripod or other stand at a known fixed distance from the subject, set the camera to the macro mode indicated by that distance (either MACRO or SUPERMACRO), zoom out to the widest focal length and take the shot to see if it is clear or not.
If so, your camera probably has no problem. If it is still not focusing properly you might want to send it into the service center for a diagnostic. There is no charge to diagnose a problem with your camera and if nothing is found to be wrong you will only be out of the shipping charges spent to send the camera in to the service center. If a repair is needed, it can be done at that time.
1. Do not use the zoom while using macro.
2. When clicking the Macro button, click it again, only for 2 more seconds at the second click, it goes to 'Super macro' mode for zero distance. This works in the Canon S3 IS, I hope it will help you in the older S2 IS.
3. Use a tripod.
4. Use the timer for no movement when using a tripod.
5. Try using the manual focus, it does the trick when the camera doesn't focus automatically.