When I first saw this I thought it was probably just a shadow being cast by the chemtrail.  But I've seen the phenomenon several times when the position of the sun was such that it was obvious that the line could not be a shadow.

Some investigators think these dark lines are strongly indicative of particle-beams which would be greatly enhanced by the addition of aerosol metallic elements.

So far, it appears to be a mystery and we can only speculate on the reasons and causes.

Videos:

Black shadow guided plane-- I just watched this for the 5th time and was surprised to see what appear to be 2 orbs (ufo's?) go flying by at high speed at 32 seconds.  Rerun it a few times (try pausing) and check it out!

Chemtrail spraying across a shadowy black line

Chemtrail Planes Very Close  The narrator doesn't mention it, but a black line manifests toward the end of this clip.

Black Line

Black Chemtrail

Black Line #2

Chemtrail Central photos and discussion http://www.chemtrailcentral.com/ubb/Forum1/HTML/001795.html

Chemtrails and the 'Black Line' In Sweden  http://www.rense.com/general2/blackline.htm