I got the same problem here with Nuendo 8.2. I set a custom columns and sometimes (randomly) they disappear, sometimes it happen after a restart, sometimes even without leaving the application at all. With Nuendo 8.1 this didn’t happened, neither with 7.x nor 6.x, etc.
It’s very annoying. I agree with diode303, it should be a way to store a set of columns without creating a Mediabay aspect for each set.