Hello Andy,
I am not exactly sure what signifies the end of the calibration. In any case, the best thing for you to do is to run NI-Spy in the background when you are running your Rocky Mountain Basic program to see what commands are executed with what parameters. Do the same with your C code. If both programs are the same, then the spy captures should also look the same.
NI Spy TutorialThese two example programs may be of use to you when analyzing your spy captures.
Compare the Differences Between Two NI Spy Captures *requires MS Visual Studio* *Note: Use a simple compare*
Convert an NI Spy Capture into a Spreadsheet File
*helpful for reformatting spy capture for easier printing*
http://zone.ni.com/devzone/devzone.nsf/webcategories/BFEA3A69F40A9F8C862569FD006FFCF6?opendocument&node=DZ59203_US