Our products are Ion Beam Deposition and Etch tools, operating at extreme vacuum. As part of the final inspection "pump down" times and "leak back" rates are recorded and compared with specification. The data is accumulated by the tool's software, comparing the vacuum level over time. The software runs all the hardware and process parameters of the tool, this is just a very small utility available as part of the package.

My question is whether the software should be considered a monitoring and measuring device and controlled under Sec. 7.6.

I would consider it M&TE when considered as a whole. That is - the test device and the software are technically 1 package or 'box'. You calibrate or standardize it as a system, not as individual pieces.