AFAIK, and according to some emails I exchanged with the maintainer, doing the right thing with image metadata is a PITA. There are many formats, each one slightly incompatible with the other... and it's easy to get trapped.

Moreover, the MakerNotes has additional issues, and it's clearly stated in the docs that it might be read as a whole block instead of single items. Try to see the MakerNotes option (that defaults to 0, i.e. "Do not extract writable subdirectories"). Even worse things can happen if you play with the preview, because this seems not to be guaranteed to be small enough to make all the image formats happy, and tends to be left out when copying metadata from one file to another (e.g. to restore metadata on some photo you have worked on). You have to go through some loops to get the data back safely.

The bottom line is that Image::ExifTool is a wonderful module, but it has quite a few glitches when it comes to writing metadata, especially MakerNotes ones.

Last, but not least, take into account that exiftool (the program) generates "fake" metadata as well, taking as input stuff like file size, file date, etc. These tend to be read-only, so don't lose too much time trying to modify them.