No ePub file can be uploaded to iBooks anymore!!

SInce 9.3.1 update iBooks failed to recognise ePub files transferd via third party apps like air transfer. Also, my book orders and categories changed suddenly and entire library is becoming a mess. Books took strik more times to open and many bizarre things happened to iBooks. Apple please fix this issue. Because for many of us iBook is a major selling point for iPad.