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Depending on what you are shooting and the conditions you are shooting in, this could be related to AF. There is a CF setting that affects the speed with which the first and subsequent shots in a burst will fire. You can set either of these (first shot, later shots) to focus-priority or release-priority. When set to release-priority, the shutter will fire whether or not focus has been achieved. With the other setting, focus must be acquired before the shutter will release. In settings where focus might be more difficult to achieve, if you have first and later set to focus-priority, this could slow down the frame rate. Of course, you may already know all of this, but you didn't mention it, so I figured I would.
A second possibility is that the card you are writing to in the camera isn't fast enough to keep up with your shooting. If you're shooting jpg, this doesn't seem likely, but a slow card definitely could hang you up.