I have the Canon 180 Ian, not the Canon 100 Macro, which I believe Doddy has. The canon 100 Macro has an awesome reputation, so I seriously doubt there's anything wrong with your lens. Macro is very frustrating and demanding - you can usually expect to take lots of shots for the bin before you get a good one, particularly hand held, as you're often struggling to keep the subject in the viewfinder let alone in focus.at that degree of magnification.Using a tripod and focusing manually is usually the best approach, but if the subject is moving then it's usually a case of going hand held. My hand held success rate lept up when I started using hi-speed sync with the 580EX and I know Doddy's did too.
Here's my dodgy explanation of how it works...
SLR cameras have a focal plane shutter which consists of two blinds. The first blind moves across (or up) to fully expose the sensor, and the second blind moves across(or up) to cover the sensor when the exposure is finished. There is a limit to how fast a shutter speed can be obtained while fully exposing the sensor for the duration of the exposure - usually around 1/200th or 1/250th of a second, although some DSLR cameras manage up to 1/500th. It's this which determines the maximum flash sync speed of your camera - in the caseof the 20D -1/250th of a second. Up to this speed the whole sensor is exposed when the flash fires, and your subject is evenly lit. The actual flash duration is very short, much shorter than the time the shutter is actually open.
When you wish to use a shutter speed above 1/250th of a second (20D), the way your shutter achieves these speeds is the first curtain starts it's travel across the sensor exposing it, but before the sensor is fully exposed, the second curtain begins to follow it across covering the sensor as it goes. The effect is of a moving slit ( the gap between the two curtains) travelling across the sensor which exposes the whole sensor for the required time, but incrementally. As the shutter speed gets faster this slit gets narrower all the way up to 1/8000th of a second. Obviously your flashgun cannot sync with this moving slit - the flash duration is so short you'd have just a narrow band of your shot properly lit by the flash coinciding with wherever the slit was in relation to the sensor when the flash fired.
Hi speed sync is a modern marvel which pulses the flash output from the flashgun in a series of stroboscopic bursts all strung together, which continue throughout the travel of that slit across the sensor, so that the whole scene is evenly lit. Hi speed sync has it's limitations in the distance at which it can operate, so it's best to keep it to reasonable close-ups and a fairly large aperture, except for very close and macro shots where it's extremely useful, but for best results you'll need to increase the ISO as those pulsed flashes are much less intense than one big whack from the flashgun. You'll find you can use a fairly small aperture, but you'll need to experiment to find how small you can go before you get under-exposure.I'd also make sure your flash batteries are fully charged to get the best out of your gun with this technique.
This was a tripod shot with the 580EX mounted in the hot shoe. A macro ringlight would be a big help in eliminating shadows and getting even light distribution, Because I was using a tripod I was able to auto focus right on this guy's head, and he wasn't moving, but for hand held shots and moving subjects you have little or no chance with autofocus.