I've noticed in some themes, the SMS icon is called SMS.png or Text.png, where the native app now uses the name Messages.png. I've had to change the name of the .png in DiskAid to get them to display the new icon instead of the default.
You can change it via iFile or possibly even MobileTerminal, as well, right from the phone. It's just easier for me going in from SSH/DiskAid.