Even if you running program as root, you still have to use ioperm() to enable port access. For more details see for example this HOWTO: http://tldp.org/HOWTO/IO-Port-Programming.html it seems that the HOWTO explain how to compiler an application in linux native but I've already an application in binary (exe). I've see that are more version of wine that the windows API used to enable i/o permission in winXP is corretly implemented (win32). WinXP Driver dialogs with this API to enable i/o. Can I implement directly in my application the permission to use i/o so I can use it in winXP and linux (as root)? The program to run as root is the application or wine? es: gksu wine myapplication can work?
