I have no idea if this will help as I sync via iTunes under OSX.6.8 - but there may be a clue somewhere here:
I have to say that, even after doing all that, my problem seems to recur at random with no obvious trigger - and it is even more bizarre because, like you, not all calendars or events are affected. Sometimes, different events within the same calendar are duplicated whereas others aren't!
And just how the iPad seems to pick up events which no longer appear in iCal is beyond me - presumably somewhere in a plist or old cache file but, as I said, no-one has any idea what or where!
No-one has managed to explian why my problem occurs or, indeed, just what is happening, but at least I now know how I can correct it, albeit via tedious series of steps.
I hope that helps?