Contrary to many other camera manufactures Canon has placed the focus motor in the lens instead of the camera house. This means that every Canon lens has its own focus motor which fits exactly to the specific lens. Just for that reason the file format can never have any influence at all on the focus speed. The reason of a slower AF could be that the target is difficult to get in focus etc. a target with very dark colours like a Blackbird or a clean white surface. Also poor light conditions can make it slower. The AF focus by looking at the difference in dark and bright areas. Let me give you two extreme examples:
1. On a Tiger in bright daylight the AF will work fast because of the contrasts.
2. On a Dark subject in poor light the AF will work very slow (or not at all) because of missing contrasts.