The problem with MecksUnit not mocking modules in some cases is related to this issue: Mocks are not found when running "mix test" with non-path arguments · Issue #4 · archan937/mecks_unit · GitHub
It works fine only when the mix task is run without arguments or when the test file is present among the arguments (which is the experience you describe).
Also working in version 1.2 and not working in version 1.3 points to that this was introduced in Force sequential ':meck'-ing to tackle parallel compiling errors · archan937/mecks_unit@12862b6 · GitHub.
