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I would be turning long exposure noise reduction off and changing high ISO noise reduction back to normal or disabling it entirely. While I have no experience with the 7D, with my 5D mk II and 60D cameras, having particularly the high ISO reduction on visably reduces the quality of the image. This may be the cause of your issue. For individual shots you are better of doing noise control in post processing like you say you have. Timelapse movies are very forgiving on noise in the individual images. It barely shows up in the finished film.
Cheers
Greg
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