Now I tried the chrome extension EPUBReader and the ligatures where shown correctly. I also tried the Calibre 4.5 viewer with the same font preferences I had used with the 3.48 version. But that made no difference, the ligatures (mostly "ll", but also "fr", "ft", ...) were still not shown correctly.
The e-book I used is "Hoffmann - Werke v1.0.epub" from
https://www.mobileread.com/forums/sh...d.php?t=192411.
So it's still a mystery ...