Okay, that is strange. If I follow your instructions (I am testing on Ubuntu 12.04) and open your test file, then the custom node and edge data is always imported correctly.
Maybe that is a strange problem with some custom settings. Can you zip your profile directory and upload that one, too?
When you open test.graphml via "File" -> "Open", you do choose the right file and not some other (older) test.graphml file without custom data that is not located in /tmp, right? I am asking because your screenshot shows a hierarchic graph whose hierarchic structure is different from the hierarchic structure in my screenshot. Of course, this difference could be due to different layout settings (I used default settings) or manual modification.