Try toggling a Full System Scan at the Launcher. Toggle it where you enter your name and password, not on the EULA screen, and see if it requires patching. it is possible some of the files in your game directory need to be updated.
You may also want to go to your MxO directory (C:\Program Files\Monolith Productions\The Matrix Online\ by default) and look for your Profiles folder. Right-click this folder and choose "Rename" and name it "Profiles1". Try to log in again after this.