I think it is a backend problem..
This line gave me the hint
I also noticed that instead of a tree of PAGES to select from, I get a tree of all SECTIONS to select from. Since every page consists of 4 or 5 sections, this makes it very difficult to find the correct link.
I guess the 404 page also has another module that builds a page-list (section-list in this case) for some selection.
To prevent slow loading in large website, the pagelist is stored in a variable and if that variable exists it will be re-used.
The variable name is a little bit generic ($links), so it is possible another module uses that already.
Now, you select a section_id and this section_id is used as page_id to find the correct page.
Since section_id's are alway much higher than page_id's the result will be unpredictable.
I must admit, it is bad programming
I will do a quickfix in a next version.