As you know, LEEDusers had reported issues with new LEED-2009 Materials and Resources Calculator (v06) almost immediately after USGBC issued it in January 2016. There have been several posts on the 2009 NC and CI forums (http://www.leeduser.com/comment/redirect/62905) .
On April 8, 2016, USGBC issued a revised version of the Materials and Resources Calculator (v07). For now, at least, we can download this spreadsheet from http://www.usgbc.org/resources/materials-and-resources-calculator-v2009. There appear to have been some modifications, but I suspect that v07 does not resolve all the issues that were raised concerning v06.
I hope that USGBC will address the 2009 MR Calculator when they release their article clarifying the recent updates to LEED Online forms and calculators.