I have no idea why clock settings would matter, other than there may be some other configuration setting getting saved whenever something is changes (such as setting the clock.)
Epubs opening in one reader but not another is usually a symptom of a non-standard epub. Some readers are just more forgiving when the files aren't quite right.
I notice you are only having problems with the epubs you stripped the drm then edited. Try running the documents through a validator such as
http://www.threepress.org/document/epub-validate/, and see if it catches some bad tag or something.