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DirectX issues
First, make sure you are running DirectX 7.0a or 8.0a, as versions 7.0 and 8.0 have DInput problems which were fixed in their 'a' counterparts. You can get the lastest DirectX from http://www.microsoft.com/directx If that doesn't fix your problem, delete the ePSXe Configuration registry entry under 'HKEY_CURRENT_USER\Software\Epsxe\Config' using Microsoft RegEdit, if you find that too hard, I suggest a powerful, yet easy to use registry editor, RegCleaner (http://www.jv16.org ). After deleting the entry, reconfigure your controller (and everything else =P) in ePSXe.
Problems with Force Feedback (answer provided by Wormie )
Some people seem to have troubles getting Force Feedback to work for them. During testing, we found out that this feature only works when the controller is set as analog/digital in ePSXe's controller setup. Also, when setting up the analog controlls, messing with the options at the very bottom of the controller config screen is a bad idea - just setup the 4 way directional pad area with the analog stick instead of the directional pad.