You've done the steps I would recommend at first. You can try this suggestion, but if you continue to experience the pronblem, we'll need your
system information.
Try going into your Matrix Online directory (usually C:\Program Files\Monolith Productions\The Matrix Online\)
Locate the CFG files. These will have names like autoexec.cfg, options.cfg, useropts.cfg
Delete these files.
Go to the Profiles folder in this directory,a nd rename it "Profiles1"
Stat the game, and toggle the Full Scan option from the Login window (not the EULA screen).
Once you get In-Game, you can go back to the MxO directory, and remove the new Profiles folder, then rename the Profiles1 back to just Profiles. This will give you back all of your hotkeys/macros/map settings etc. However, if you experience problems logging in again when this is restored, it is possible one or more of the files int he profiles directory has become corrupt.