Zat, after following this topic a bit I came to the same conclusion of xalener. It really looks like you were selecting (and applying the texture) to more faces than you desire - I speak about where you try to texture individual faces, not about texturing all at once using a mapper.
Did you make sure that you're selecting only the faces you want to texture?
As I would do, first of all I would make sure that the faces I want to texture are exactly in front of me, rotating the view.
Then I would:
Click on "point edit" mode
Click on "face select" mode
Click on the "select" tool
Click on the first model's face I want to texture, using the left mouse button
Click on every other face I want to texture, using the right mouse button this time
Here, normally, I switch again to rotate-view mode and I make sure that only the interested faces are selected. Then I bring the selected faces in full view again and I exit the rotate-view mode.
Finally I click on the UV button, which presents me with the yellow circle of the texture tool, and there I arrange the texture by clicking with the various mouse buttons, either inside or outside of the yellow circle.
Hope that helps.
Edit:
Wait a moment... Lynn suggested just the same some posts above... did you try that Zat?