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'Run', which features an appearance from Justin Timberlake, failed the Harding Test - guidelines put in place to stop TV images causing epileptic fits.
The video is available online and Gnarls Barkley member Danger Mouse told Billboard he hopes the situation will be resolved soon.
"I don't know exactly what's going on, but we're having issues. I think [the video] is cool. It works for me. But I'm not necessarily that easily seasick. We can't predict how people are going to interpret it."
'Run' features Timberlake as a public access TV host who introduces Gnarls Barkley performing their track on his City Vibin' show.
