I was experiencing the same issue. The file selection dialog for both the Save As and Export to PDF actions did not appear, and Xournal would hang.
I deselected Use XInput in the Options menu. That fixed the issue. Both Save As and Export to PDF work for me when Use XInput is deselected. This seems to be related to upstream bug 170: https://sourceforge.net/p/xournal/bugs/170/
