There is a problem in making a part of layer in GIMP becoming transparent; that is GIMP refuses to make selection color to alpha channel. This is because GIMP 2.6 not adding alpha channel by default into a duplicate/new(?) layer. There are two solutions:

  1. You could add an alpha channel to the layer then do things like previous version.
  2. You can add a layer mask and do it from that masking layer. This will complexing things up but will gives you unlimited undos/redos plus your original picture is unharmed, which is a good practice.

REFERENCE:

[FLG]  http://www.flickr.com/groups/gimpusers/discuss/72157612736720804/