you can apply the auto-STF (or any STF) to an image by:
1) dragging the STF's triangle to the bottom of the HistogramTransformation window (to the strip where the HistogramTransformation window's own triangle is)
2) applying the HistogramTransformation to the image, either by dragging the HT triangle to the image, or if the image is the topmost window, by clicking the blue square.
after doing this, it's a good idea to reset the HT (4 arrows in the bottom right corner of the window) because the STF->HT manipulates the R,G,B channels instead of the combined channel and that can lead to confusion afterward.
don't be surprised if your image goes all white after this - that's because the STF is still applied. just turn it off after applying the HT.
you are not the first person to be fooled by this, but as sander says such "screen stretches" are a part of any good astro processing package...