qmake could not resolve Info.plist, sometimes

When qmake generates Makefile, it sometimes complains:
"WARNING: Could not resolve Info.plist: '../../../lib/qt-5.2/5.2.0-rc1/clang_64/mkspecs/macx-clang/Info.plist.app'. Check if QMAKE_INFO_PLIST points to a valid file."
(The ../../../lib/qt-5.2/5.2.0-rc1/clang_64/mkspecs/macx-clang/Info.plist.app does exist on my machine)

While, with another almost identical project (with different folder name), which does not complain this warning. This error caused the Info.plist not copied to the final bundle, thus the compiled application would show up as non-hires in Retina Macbook Pro.

I looked around a bit, and found that when it's complaining, the Makefiles generated are using relative paths for include/mkspecs; comparing to when it's not complaining, the Makefiles are using absolute paths.

It looks like a weird behavior to me. Lemme know what further info I can provide.