The issue was discussed shortly here in the bug report (post 146, 147):
https://www.mobileread.com/forums/showthread.php?t=80381
and in other threads, too, but I couldn't find it. Maybe it was in the German part. I myself had the problem only in the beginning, when the point "library" from the main menu brought me to the library and not to folders. Since I'm only using the folder view the problem doesn't occur anymore. I can imagine that after deleting some books the system is calculating the database anew and that this needs some time. As I said before, only some users mentioned this problem.