Have a look and see if it went into your library. I just opened a PDF that was emailed to me and it didn't open automatically. It was in my library and opened when I touched it.
I'm at a loss as to where it may have gone. Sorry I couldn't help with this one. Let us know if you manage to do it. I, for one, would be interested in the outcome.
When you state it won't open in iBooks what exactly is happening when you make the attempt?
Are you receiving a message of any type? Does your attempt result in the currently active app (whether it be email or a native or third party PDF viewer ) closing and you being returned to the ipad desktop? Do other "Open In" apps like kindle (if installed) or Quick Look open the file without issue?