Just to narrow down the details...
Was the Delineate option specified in layout setup? If so clear this option and see what you get.
Were the field borders specified as complete borders (all for sides) or just for certain sides of the field?
This las one is a known issue, but you should have seen it with PDF's and not when printing---the opposite of what you report here.
Delineate is not selected. I took another look at the layout and realized my initial commentary was incorrect, the bottom line of the field is intended to be printed as a divider between the next record.
I believe you answered this question. I assume FileMaker will have a fix for this in a coming update?
Yet what you described is the reverse of the bug report: They see the issue in PDF's and not when printing.
For More Information see: FM12 Save as pdf Issue
This is one of many acknowledged bugs that can be found in the Known Bug List thread here in the Report an Issue section of the forum.
It can also be downloaded as a database file from: https://www.dropbox.com/s/jt09b82i0xijbu3/FMP%20Bugs.zip
I don't work for FileMaker so they will have to speak for themselves. Previous "policy" statements will tell you that they do not announce what bugs will be fixed in an update in advance of that update's release.