Why does updating my MTGO always comes up with protocol errors?
Solution 1:
There is a FAQ for the most common MTG-Online errors here: http://community.wizards.com/go/thread/view/75846/27085537/MTGO_Technical_Issues_FAQ!_*Start_Here
For your protocol error, as Krazer stated, the recommended fix (See also section 1-7 in the link above) is listed as such:
Delete the NewFilelist.txt file located in the MtGO directory, then start.