Do you have long exposure noise reduction enabled?
Menu -> Red Camera #3 page -> Long Exposure Noise Reduction
When you take a long exposure with this feature enabled, the camera takes a 2nd exposure of equal length but without opening the shutter. This 2nd frame (a "dark" frame) is used to assess the noise levels so that the camera can reduce noise by subtracting it from the original frame. However... it also means all long exposures actually take twice as long before they are ready.