Well, I don't execute mad qmake, I'm using QtCreator which executes qmake from freemantle directory itself. Executing qmake from the same location manually (that is, cd'ing to directory where .pro is located and then invoking qmake with absolute path) has the same effect.

Regarding your results, are you listing those headers in HEADERS variable or does qmake find them as dependencies itself?

I found that automatically found dependencies are generated correctly (thanks to Joorin for an obvious solution), and only those headers that are also listed in HEADERS are affected.

I'm also using more than one level of ../ indirection, which may or may not affect the results.