Originally Posted by ectoplasm
I can't offer any help for your specific case, but I can say that I use Sigil on about half of the epubs I read, to tweak alignment or paragraph spacing, etc. The modified books work in Coolreader for Android, Linux, and Windows. There are some rather vague settings in Sigil which can affect how it reads/writes files.
That's interesting because I just download CR for Windows and have the same problem. I was about to conclude that it's a Nook or n2a problem but now that's not the case.
So what are the "vague setings"?