OK, R2 is no longer supported...
What you should do is update your app to use CR Assemblies version 13, you can get the VS installer and runtime here:
SAP Crystal Reports, developer version for Microsoft Visual Studio: Updates & Runtime Downloads
SP 9 will support VS 2013, due out in a few months or less.
So right now we don't have any suggestions for you, R2 is not supported in VS 2013.
As of SP 8 you can get the paper size ENUM that is saved in the RPT file, everytime you add a custom paper size likely you'll get a new ENUM for it. As you can see CR saves the ENUM, that is likely your issue.
In SP 8 you can get the Custom Paper size by name and set the ENUM accordingly using the CopyTo/CopyFrom API so it updates the report info using RAS or the Engine.
And I believe if your printer doesn't support custom paper sizes how can you define one so CR uses it? The System.Printer collection won't have an ENUM for that size...
Don