madge does not detect all circular dependencies or even all files with circular dependencies. I think this is a fundamental issue with the algorithm in cyclic.js. (There may be some good suggestions in here: https://stackoverflow.com/questions/546655/finding-all-cycles-in-a-directed-graph)

I created some minimal test cases here (including graphviz diagrams in case that helps):

yoz@847668f

Explanation:

• "defg" case: There are two cycles: d -> e -> g -> d and d -> f -> g -> d. However, madge never reports the d -> f -> g case (or indeed that f belongs to a cycle), regardless of which file(s) we use as the starting input.
• "bcdeg" case: There are two cycles: d -> c -> g -> d and d -> e -> g -> d.
  • This is equivalent to the "defg" case (but with 'c' instead of 'f'). Yet the madge output is different - it finds all the cycles.
  • But if we add a dependency b -> d and start at b, madge no longer reports one of the cycles.