Thanks for sharing this.
When using the console tool, where do you see the reported number of tests? Is this in the HTML report exported from the tool, or perhaps something inside the trace output?
There are several different ways of counting tests. For example, one method may include fixtures as being physical tests, while another disregards fixtures and only counts child tests. Then there are ignored tests, tests excluded by engine mode, etc.
The difference between the clean vs non-clean workspace is interesting ... are you able to narrow this down to the 4 tests that are different? Note that NCrunch's console tool will completely rebuild new NCrunch workspaces for each execution, so in this case there may be a difference in the source itself.