They were out of sync before, so they probably show incorrectly in the cms as well now.
There is really no way to fix the problem without breaking it in some places that were encoded improperly in the first place.
At this point you will have to find and fix those pages improperly encoded in the past. The issue will be fixed moving forward I believe, and you can re-enter the improperly encoded characters now and they won't be an issue anymore.
I think now the character will show the same when entered through the CMS, through phpMyAdmin, and when displayed on either site. Until this update they would always be broken in one place or the other, but unfortunately any special characters entered in the past will still be incorrect in one or more location until re-entered now that the problem is fixed.