For starters the original video that Mchapman posted hand not been tampered with and or photoshoped. It is the original Naudet video and i come to that conclusion by simply comparing it to a few other Naudet posted videos. So atleast thats a credible start.
Here is an HD version of the video i will be using in my post.
http://www.youtube.com/watch?v=NKyNl26s3ic&feature=related&fmt=18
As for the black line that was in question. Mchapman was correct when he stated it seems to appear out of nowhere 15 seconds after the initial impact, well actually its more like 12 seconds but im not holding you accountable for that because its irrelevant.
As for the rest of your post/ideas on the issue you seem a little off. Clearly without even having to inspect the videos im sure everyone here was well aware that the reason it seemingly appears "out of nowhere", is because of the dust and debris finally clearly after about 12 secounds.
As you will notice from watching your footage at around 18-19 secounds the amount of debris and smoke in the Air is drastically clouding any clear shot of the building. All detail is lost behind the smoke and truthfully you can only really make out the building outline and fire from the explosion.
At around 20 sec you will receive a shot of the towers from a distance that shows the fog and how much it is clouding the shot of the Camera.
Now at 23-24 secounds you receive your first glimpse of the mysterious black line appearing from behind the dust cloud. Now compare the screen shot at 20 secs to the one at 23-24 and notice the significant difference in color and visibility. This is because the debris and dust are finally starting to blow away and reveal the damage for the first time. This is where you notice your black line.
The funny thing about this black line is that it is actually a trick on the eyes which is more visible from a distance then upclose. (Yes weird) That is the reason for the close up in your video not showing the black line.
I came to this conclusion after watching several videos of people zooming in and out of the towers and noticing how when they zoomed out the line was clear as day, but when they zoomed in the line magically disappeared.
This is only true for the earliest shots of the towers. As the day progressed and the smoke became darker and more parts of the WTC began to pour smoke, the building does become scorched and the lines become more permanent and noticeable.
Shadows and lighting also seem to play a part of this line appearing darker and more prominent in different videos. Its all about the shot and the angle its taken from.
Dont believe me? Try and look for yourself.