Hi Edwin

Your black parts could be down to several things.  I have had some black parts on the -200 repaints.  

FS Repaint only uses the fallback file for the base aircraft  IE.  Doing a -100 repaints is ok as the fallback doc points to the base  737-100 folder.  A -200 repaint also points at the 737-100 folder.  This causes black patches on my aircraft two.  That's the reason I did in game screeshots of my Air California 737-200 repaint.

It could also be down to the alpha and specs too.  The biggest patch I get on the -200 is where the landing lights reflect of the airframe.

You could make a repaint only folder which contains all the textures that are found in a repaint and from the folder named "texture".

Just a thought.