this is a known issue and already being fixed in one of the embedded packages:
this only happens with open contours...
a update is scheduled soon
after you run the script, you'll need to close and reopen the font for the change to take effect. (I've just tested it again in RF3, works fine)
another solution would be not working directly on a server or DropBox folder, if possible. you could ‘check out’ the font to another place, edit, and then check it back into the server. (or use a version control system like Git, which works just like that; see this tutorial in the new docs.)
So after running ufonormalizer on the files things seem to work. It takes a really long time to compile (about 10 minutes, though that drops to about 1 or 2 minutes if I turn off autohinting), but it does work. I'm not sure what ufonormalizer actually changed (it looks the same to me) but nothing crashes and there is a working OTF at the end of the process.