The MySQL patch only fixes a problem where you have a TEXT data type in your MySQL table and save Unicode characters to it.
On the other hand, updating references is a constant problem. To update references I would remove any references in my project, and re-add them using the Browse tab, not the .NET tab. The .NET tab acts more like a reference MRU, and often will just re-use any old, out-dated dll that it finds.
David Neal Parsons
www.entityspaces.net