Well I had added support for parsing the Maker note of Fujifilm cameras and thought this was a better number to use for the frame number (than defaulting to last 4 digits of filename) since there was no other place in the file where Fuji was setting this (unlike some other models that put this value in their Maker note). But looks like it is indeed the number used for resetting. I've removed this and it now gets the frame number again from the filename. This fix will be in the next update. If you send me a PM I can get you a version to test against.
NOTE: if you expect to use this frame number and also rename your files, you will need to tuck away the frame number in some unused IPTC field during ingest. For example put the {fnm4} variable in the special instructions field (or wherever suits you).
The good news is that PM now picks up the internal serial number (a really long string), white balance, sharpness, contrast, and focus mode (auto/manual) for Fuji in case those values aren't written in the standard Exif area.
--dennis