Did you received some help from forum?
I have the same situation here (same OS, version, bits, mono) and exactally the same error.
I just opened the beam example and tried to save it with another name.
Looking for the diff between the files, my is broken in the middle, have different xml patterns, like missing slashes, but still valid.
The saved file is pretty similar to original example file until line 1017, where the new one is broken.

flcs@flcs-desktop:~/SMath$ mono SMathStudio_Desktop.exe

Unhandled Exception: System.NullReferenceException: Object reference not set to an instance of an object
at SMath.Control.PlotRegion.ToXml (System.Xml.XmlTextWriter writer, SMath.Control.FileParsingContext parsingContext) [0x00000] in <filename unknown>:0
[ERROR] FATAL UNHANDLED EXCEPTION: System.NullReferenceException: Object reference not set to an instance of an object
at SMath.Control.PlotRegion.ToXml (System.Xml.XmlTextWriter writer, SMath.Control.FileParsingContext parsingContext) [0x00000] in <filename unknown>:0

I'd like to read or debug the source code try finding out where it's bugged.
It seems like persistence of objects to xml is the problem.
Some new structure created at PlotRegion objects design (in source code).
Maybe an inconsistent pattern or relation between objects, I suppose.

But your post was 3 months ago with no answer.