What's the difference between "M" and "geNorm M" in qbase+?

The M-value calculations are identical and described in Vandesompele et al., Genome Biology, 2002. The M-value in the reference target stability window is determined using all reference targets and hence reflects the relative stability of all appointed reference genes in that particular experiment.
This is typically the place where you investigate if the previously validated reference genes in your experiment are (still) good (on average 2-4 reference genes should ideally be used for final normalization in a given experiment).

The geNorm M value (geNorm analysis) is slightly different as it denotes the average M value of all remaining reference genes upon stepwise exclusion of the most unstable reference gene (highest M value).

Figure: Average expression stability values (M) of remaining control genes during stepwise exclusion of the least stable control gene in the different tissue panels (black circle, neuroblastoma; white circle, normal pool; white square, bone marrow; black square, leukocyte; gray circle, fibroblast; gray square, systematic error).

 

The geNorm module is typically used for assessing the stability of a large set (ideally 8 or more) of candidate reference genes. This is what we call a geNorm pilot experiment.