https://codereview.qt-project.org/#change,62937seems to have a patch that is working to solve the 10.9 Modal sessions issues on Mac.
EDIT: the current build script is using a precompiled version of Qt, targeted at Mountain Lion. Maybe try building Qt from scratch (using the homebrew formula for inspiration) and adding this patch.
etotheipi found that patch a few days ago. I already modified the build script to build Qt from source. Requires the git head and 2-3 patches just to compile. Unfortunately only to find out that the patch you referred to makes no difference. My guess is that the patch does not solve the actual problem, but only the symptom, and that the real trouble is elsewhere (possibly in OS X and not in Qt).