Previously I have overcome this problem by doing the following:
1) Store all settings in a "settings" class.
2) Create a private bool member within the form to track the state.
3) Pass the settings class to the form.
4) Once the settings are passed in - either on the constructor or in the
form load - propulate all controls with the information.  Set the bool
member to "true" indicating that your population of settings has been
completed.
5) In the on change event of your controls (and I assume you share a common
change event among all the control) - first check the member variable to
ensure it is set to "true" before enabling the Apply button.  If the member
is still "false" - then do nothing.

I've also heard of people putting all there event declarations into a single
method and then not calling the method until all the data on the form has
initially been populated.

Brian Patterson
http://dotnet.redeyepos.com
http://brian.redeyepos.com