It looks like this is a fairly common issue amongst developers compiling apps for windows.
There are directions above on how to circumvent the check, but they refer to adding a registry value with an installer script, which I'm not sure is editable in the filemaker runtime apps. If you were somehow able to add this to your CD's autorun routine, you might be able to solve this issue.
Otherwise, it's not harmful (as far as I've read), does it happen for all users or just some users? Have you tried copying the files over from the CD to a local folder and starting it from there?
Thanks Mike. I'm glad to hear it's not likely to indicate a fatal flaw in my program. I hadn't thought of making an autorun, I will try to do that.