Seeming as I have to repeat my answer on this time after time I'm gonna write how to uninstall arma. I will make this for all those people who put addons in their addons folder.
When you patch arma and install arma you should make sure that there are no 3rd party addons in your addons folder. You should always use modfolders.
How to perform a clean install.
1. Make a backup of your mods and addons that you want to keep and store them in a safe place like My Documents or something.
2. Go to Start>Control Panel>Add/Remove Programs from there you can choose to uninstall ArmA.
You can also uninstall AmrA by locating the install wizard at Start>Allprograms>BohemiaInteractive>Arma>Uninstall or Start>All programs>Atari>Arma>Uninstall. Uninstall the game.
3. Go to your ArmA directory and manually delete the ArmA folder. This will clear all subfolders inside like Addons and Dta which may have remains of 3rd party addons from your old installation. It is important that they are deleted so your new installation will not be corrupted and you will not encounter any errors.
You need to delete the folder where you installed the game, these are the most common folders where the game is installed and would have to be deleted:
C:\Program Files\Bohemia Interactive\ArmA
Delete the folder named "ArmA".
4. Insert your DVD or execute your Arma installation file to reinstall.
5. Use mod folders this time. :|
Added to the FAQ, thanks for writting this :)