Are the numbers only changing in the context of Coverage, or also overall size (in the list of metrics to represent on the activity graph, choose Custom > Lines of Code
That does look odd. Normally we would suggest that this is the result of not doing a clean/full build, but we can see in your MSBuild command that /t:rebuild is specified.
Is it possible that somebody else is targeting the same project key but could be using different commands than you?
Are you always targeting the same project (.csproj) with your MSBuild command?
If you are able to manually execute two builds that produce different results (and have the logs of both), my next recommendation would be to do a diff on the logs (even using a tool like https://www.diffchecker.com/) and understand would could be different (besides the timestamps)