I posted a similar topic a while ago, the issue still persists, and I made quite a bit of calculations on the second board and wanted to at least save it as a pgn and might have stumbled on what might be causing it.
Clicking on the download button, all the pgn says is
[Event "Just for Fun
The name is "Just for Fun <1600", so maybe some symbols ( in this case the <) in the name are causing a corrupt and empty pgn, so it is actually saving, it's just that the pgn can't be formated, because it thinks there is a comment or something and loading the pgn leaves the second board empty of variations.
If that's the case, could the affecting symbols be replaced before saving into a pgn or not allowed in tournament or game names, etc.