OK ... this is bugging me into action again. Here is an example (very simple board) that shows the bug. If I save this with pattern marking set to Main = RefDes, Additional = None, all is fine. If I set Additional = Additional... and choose the custom field I've put in called "Caption", then save it - close it - open it, all is messed up. The Main marking is set to Caption, Additional to None.
I hope you can work this into a release coming soon, or tell me a workaround.