On my A720IS I am having this problem also. The canon file numbering menu setting is now and has been Continuous. I have shot a few RAW photos, they were numbered CRW_0020 thru CRW_0025. I've also taken over a hundred .jpgs since I got the cam and started using CHDK last week. Yesterday I moved all files from the DCIM\100CANON folder to the hard drive on my PC. Today I took some pics (no RAW) using the same card, all jpegs, and the file numbering of the 18 images started at IMG_0008.JPG.
I just moved those 18 images off the card. Took some pictures with CHDK disabled, Canon File Numbering menu option set to continuous and the file numbering began at IMG_0001.JPG