could you upload the kicad board (only edge if you prefer) in e.g. dropbox or similar?
I would check if there is some prob in the board edge…
it is strange I did not have any prob with IDF export …
(Cirilo has done a great work with IDF 
)
I usually do it with a lot of non ‘regular’ edges…
Have you tried with the RC version?
In which OS are you working?
and which version of FreeCAD?
Note that the IDF export requires that you have a ‘closed edge’ board… I mean if you see correctly in 3d-viewer your pcb edge, you should get a good IDF exporting…
if you are involved in exporting kicad board and assemblies in mechanical CAD, you probably could find useful my script kicad StepUp
it is a useful script for ECAD MCAD collaboration process…
You can find some discussion in this forum at:
kicad StepUp at the forum
moreover, if you need 3D STEP models you can download some done with parametric scripts at:
FreeCAD 3D model parametric generator
and a discussion at this forum
Maurice