This is a new one… Can you share the sequence file (.sgf) so we can take a look. Maybe it is specific to the sequence? Not sure… SGPro has been around for a good while and we have not ever had this report.
We have had some problems, in general, with Z value ordering. There are known issues in .NET applications especially with COM (ASCOM) interoperability. We would need specific examples (with order of operations and exact windows that are misbehaving) to try and chase them down.
We can’t help without logs. Please see this and we’ll try to help out.