Most DirectX programs contain their own Preset list/manager within the plugin GUI (Whereas VST's file management is usually placed within the host's wrapper/interface allowing direct access). This is not neccasarily a Cubase specific problem. If you can't access the files at all in cubase (via cubase's own interface or the plugins GUI), you may be forced to open the plugin else where and copy the settings (via Pen and Paper.........The old fashioned way).
What format were your original presets stored in???
If they were stored in a proprietary format (via an old host), that me part of the problem too.
Let us know what plugins you are having a problem with and/or what programs you created your presets in.