a540 is a vxworks cam, so it will have PS.FIR and DISKBOOT.BIN
If you delete both of these files, that should definitely prevent CHDK from loading. If it does, copy the new files. If it doesn't, you have some kind of partition problem.
A540 does not support multiple partitions, so there's no reason to have a multipartition card. If it does have multiple partitions, that could certainly be a problem.
Depending on your OS and settings, removing the card without using "safely remove" / eject / unmount in the OS can result in the files not actually being copied.