I think I see what's going on. I don't have access to a card reader at the moment, but I do now see a DCIM/ directory alongside CHDK/ in the File Browser. Tell me if I'm wrong on any of this:
The File Browser is browsing the large FAT32 partition, not the smaller FAT16 one. The directory hierarchy under CHDK/ has nothing to do with the one I placed on the small partition; rather, it is a new, empty tree created by CHDK when it first started up. CCHDK.CFG is visible because it was similarly created by CHDK on the larger partition. And everything on the smaller partition is inaccessible.
So, what, then---the small partition should basically have DISKBOOT.BIN and nothing else? Also, is it "the way things should be" that the CHDK directory live on the larger partition? The wiki's Bootable_SD_card
page led me to believe that the first partition was meant to hold all the CHDK-related files, when it suggested a size of 16MB.
And when you say that the CHDK and camera can only see one partition, is that a broad technical limitation, or merely the effect of the multiple-partition-support bug? (I.e. is this just the way things are, or a bug to be fixed?)