I'm not saying this is a solution, but something to consider as this issue can be related to grouped parameters set by type. The Group by Type is the default setting when users create project parameters. Changing these to instance based, stopped our problems of groups ungrouping.
1. Open DiRoots Paramanager.
2. Right-click and select groups
3. Sort the list and select all "Grouped Values by Type" change these to "Instance" and apply.
This worked for us, your case might be different.