I have certailny noticed the issue of PDF files varying in size. I can't say for sure that it is FM related, although some of the files are created from FM. These are generally letters with some graphic component. Sometimes at least I have successfully compressed the pdf later in Acrobat Pro (save > reduced size), but of course that is an additional process you don't want in an automated system. If I come up with anything more I'll add to the post, and will also be interested in anyone else's experiences.
Try to delete all Adobe preference files, in particular the files having name starting with "com.adobe."
Then restart the computer. If the problem remain, delete again the Adobe preference files and immediately restart the computer and reinstall FileMaker.
I Have another PC running at home that had FileMaker Pro Advanced 12.0v1 installed. I went through the motions of saving to PDF and the file size was 463KB. I then ran the update taking the version to 12.0v4 and ran the save as PDF again on the exact same report, but the file generated was 3.34MB......that's nearly 700%!!!!
This particular PC has no PDF reading or writing software installed as it is mainly for games and the odd coding session so there would be no need to assume there are any other external influnces causing the issue.
My diagnosis.........PDF Compression has stopped working in between 12.0v1 and 12.0v3.