When I was writing my paper a faced some ugly problems with the eps files. Even though I change the bounding box of the files manually, as I explain before, some MATLAB figures didn’t show properly. Then searching for a solution I found a good tool to do the bounding box fixing automatically, epstool can do it with this simple line
epstool --copy --bbox input.eps output.eps
However, after this my problem remain. Then I could fix it by changing my latex statement when including the image, like this:
The clip option makes to crop the image to the bounding box.