Hmm, it's probably that you had track view disabled. I say this because it has also happened to me.
If you hit Ctrl+A when the STF interface is not visible, the STF process applies the automatic stretch to the active image, but the track view option of the STF interface is not enabled. This is a limitation of the current PI workspace: track view options cannot be enabled for hidden interfaces, for performance reasons. So when you open the STF tool, it has track view disabled, even if the image has the auto stretch applied. This is confusing and I'll try to fix it in the next version. Does this make sense?