Hi John,
It sounds as though you are doing the same thing indicated in the following KB:
Shunt Resistors in Conjunction with Switches for Measuring Current with an NI-DMM
http://digital.ni.com/public.nsf/allkb/18E4CBEE31BCC1EC86257243000F870D?OpenDocument
From my understanding of the question your method seems to be correct. If you notice anything in the KB that is different from what you are doing or vice versa, please let me know and perhaps I can help you examine it further.
Best regards,
Steven