@Groen: Thanks for explaining, I will recheck the code to see if I forgot something.
If I read well: You get it when using the File->Import Notes-menu and when using File->Save (or Save As)?
@dima_tr: I am using functions to block screen updates, I guess that I forgot to unblock them. It could be the already known bug that sometimes the DR hangs when using xournal, but I have only seen that as a combination of scribbling and full-screen refresh.
Are there more people that have seen this problem? (this helps to determine if it is related to a local something on the DR/SD-card of Groen or if it is a generic problem.) Please try to remember if the expected dialog appeared or not. Does pressing the menu-key help, any other button?