XP Pro and Media Center are basically the same OS, just with a different set of bundled apps.
But if it's a new system, just format it and install XP Pro. The drivers for Media Center should work just fine with Pro. You can also get rid of all the bundled crap software that comes with a new OEM computer which, in my experience, improves performance and stability.
I am having trouble installing windows XP pro. I cannot install the professional version on my new com puter. Is there a reason for this? I already have windows XP media center 2005. Should I even upgrade?