Recently I restored my GameEx installation that was crashing upon startup and everything was working fine until one time I loaded it and my theme is gone like the background art and stuff... It happened after I installed a program called touchmote it turns your Wiimote into a mouse/lightgun/touch simulator. I think my problem is related to this app.
EDIT: In fact it is. Be sure to turn your touch settings to off in your GameEx configuration. All will return to normal. This thread should serve as a guide for anyone who experiences this issue.