@NewbDummy - when you first imported your books, and before you edited the metadata and attached covers etc - could you read the books with Calibre's EPUB Viewer, and did the text flow correctly etc
@theducks - I'm thinking that the problem may lie with the original epubs and not whats been done with/to them since.
I downloaded a free epub, when I tried to read with the viewer it was jumbled up, I spent a bit of time fiddling, got nowhere, removed it and moved on. It was a study from a Berlin Quango, downloaded out of curiosity - eventually found the PDF version, at a Brussels Quango
BR