Consider the attached simple example.
If you run qmake on this project when the source and output paths have the same number of / in them, the rcc dependencies (ie. that qrc_resources.cpp depends on main.qml) are properly recorded in the Makefile. This includes both in-source and shadow building.
However, when the source and output paths have a different number of / in them, the dependency between qrc_resources.cpp and main.qml is not written into the Makefile.
Checked using qt.git/4.7.