The code files generated by Qt tools (moc, rcc and uic) are created outside of the $(IntDir) if the path of the input file is somewhere above the project directory.
This seems to be caused by the usage of %(RelativeDir) inside the qt*.props files, as removing it seems to solve the problem. Unfortunately I can't distribute this modification to the other developers in my department, since the files are overwritten at startup.
The attached project is a minimal reconstruction of the error. The header file should be placed accordingly to the path used in the vcxproj.
VS Build output (translated from german):