I did the same as you, applied the preset to clip in timeline
Effects panel is still hightlighted.
Sure enough... Okay I figured out what is happening. And it has to be with a custom preset (because you can't rename regular ones).
If the effects panel is highlighted, and the custom preset is highlighted, if my mouse cursor is over the text of the preset (rather than the icon) when I click and drag it over, as soon as I click down it selects the text in the preset title for renaming. So I believe it is set to where if you click twice on a custom preset it will open the text for renaming. The problem is, it doesn't matter how far apart those two clicks are, even if you click and drag.
click on the preset icon.
I think the better feature request here is allowing us to define a video transition in seconds, like we can with audio. That way it takes whatever frames it needs depending on the sequence settings. No need to change it every time we switch media.