I'll give you more information, I think I got the case when this happens. The midi device I have mapped is a Launchpad X, I did all the steps to configure it, creating a new midi keyboard and learning every button. If I start a new song and add, for example a couple of assignments like this:
You can see I have two buttons assigned to actions.
If I close S1 and start a new song it's ok, my mappings are still there, but if I open an old song that doesn't have this mappings, it gets overwritten somehow. After that if I close and open S1 again and start a new song I get this:
I hope that clarifies the issue a bit more.
This sounds like a bug to me because opening a song should't overwrite the mappings of a template or of a new song.