Here is a piece of advice that has helped me in many patcher problems:
If you finish playing MxO and It was working fine and quit with out problems, back up your matrix online directory (It's big so you will probably need another disk, It won't fit on CD).
Then if you ever have to re-install, once you are done copy you backup over the install and you won't have to patch anywhere as much.
If your client.dll messes up, back up your profile folder, then delete the contents of your MxO directory and replace it with your back up, then run the launched and patch up to date... then copy your profile folder back.
Sometimes things like viewing files in notepad can screw things up... in particular client.dll and any texture files. (I know... it's interesting to snoop around in the files, I'm not recommending it. But if you want to snoop, make a copy of the file to somewhere else then open the copy.)
This WILL ALWAYS fix any game client related issues. If it doesn't (and your backup wasn't corrupted) then the issue is with your computer or the game servers... or the patch is faulty.