Thank you for your datailed answer!
After installing your modified EbookReader, some of my epubs couldn't be opened any more. I compared these epubs to those which work and found out that the *.opf and *.ncx files in the 'bad' epubs were saved as UTF-8 without BOM and using Unix line break style (LF only) and in the 'good' epubs - as UTF-8 with BOM and using Windows line break style (CR+LF). I re-saved the *.opf and *.ncx files of one 'bad' epub using the "right' format, and it could be opened well again.
This is not really a bug, but maybe it would be possible for you to fix them...