Do you use asus aura software?
If yes, try to completely uninstall it, run some registry cleaning and find the files, which were not deleted by the uninstaller, then try to reinstall it and use the software very slowly. Please install the newest from asus.com page.
Unfortunately the aura is a bug heaven, I even uninstalled it I can not use my RGB strips because of the buggy software.
See my thread for it.
Yes i've tried all versions of Aura lighting control. You might have any registry cleaning software in mind?
Did you try connecting an LED strip to header 1 and header 2 at the same time? Is it the same result?