Update Wizard vs New Image, does it matter?

[mddubs]

I just upgraded my embedded 1.2-RELEASE to 1.2.3RC1 by writing the image to a new CF card and then loading my config file.

I'm wondering if I should have done the update from the System -> Firmware page instead.  Everything appears to working fine, but I'm worried there may be changes to the config file that I've missed.