Please excuse me if I am stating the obvious and my reply is not applicable.
Some times the basic fixes work best. So, let me try.
You mentioned you shoot in M mode and cannot get focused macro pictures.
I wou suggest you try to set the upper dial to the "close up" mode (that is the one represented by the flower). The Canon people at:
Canon EOS 1000D
Say that: "You don’t have to be a professional to shoot like one with the EOS 1000D. A variety of preset and custom modes make it a breeze to choose the proper setting no matter what your subject. Six pre-programmed Basic Zone modes can be selected on the large Mode Dial. With the "close up mode you can get in tight for stunningly beautiful close-ups of flowers and other small objects. Results are even more impressive with optional Canon macro lenses.
Hope this helps and I'm sure you will be shooting perfectly sharp images of tiny subjects in a jiffy!