If you are instaling the latest version of the software compatible with WM2003SE, there's nothing you can do about the message. Don't worry about it. :)
I've gotten that message on about 70% of the software I've installed on my X50 and not a one of them has failed to run properly. Disregard the error. I think it's probably because most of the applications were written originally for PPC2002 ... running them on 2003SE is seldom a problem.