I've got SD400's, running the latest build from the autobuild server with a script to work off the remote.
The camera is set to raw, in the same directory as JPG and file number RESET. I take eight pictures and I find in 100Canon, eight jpg files, numbered 1 through 8. BUT I also find eight CRW files, numbered 2 through 8 and 14. (the previous set of pictures had 13). File number 14 is the same as jpg file number 1.
So, somehow the first CRW file picks up the last number, then I suppose the JPG file routine decides to reset the number.....
I can rename the first file - but if a new session takes more pictures than the last, then the file 14( in the example above) causes the real 14th CRW to be lost. At this point the only thing I can do is to not reset numbers or put up with a lost shot. I prefer to use lower numbers.