“Bad name index” / “read beyond EOF” problem

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This problem appears when one of the system files of Deus Ex is corrupted, usually it's "DeusEx.u" or "Engine.u". There are three ways to solve this:

Insert your Deus Ex CD, open it for browsing. Find System/ folder and copy "DeusEx.u" to your DeusEx/System/ folder. If it doesn't work, try copying all the files with .u extension to your DeusEx/System/ folder.
Ask someone to give you the file(s).
The easiest way is to reinstall Deus Ex. If you don't want to lose the settings, move/copy User.ini, Defuser.ini, DeusEx.ini and Default.ini from DeusEx/System to a safe place during installation and when it's finished, move them back.

Thanks to Clix for the solution.