I have never had issues with saving pdfs in iBooks in any version of the iOS on my original iPad or on my new iPad. Maybe if you provide a few more detaills ....?
Have you tried quitting the iBooks app and restarting the iPad to see if that makse any difference?
Go to the home screen first by tapping the home button. Double tap the home button and the task bar will appear with all of your recent/open apps displayed at the bottom. Tap and hold down the app icon until it begins to wiggle. Tap the minus sign in the upper left corner to close the apps. Tap the home button.
Restart the iPad by holding down on the sleep button until the red slider appears and then slide to shut off. To power up hold the sleep button until the Apple logo appears and let go of the button.
Are you looking in the correct collection for pdfs in iBooks?