Sounds like it's working properly. If you issue the action while the fade is fading, the fade will override the opacity you set.
It's not so much that the fade is overwriting the fade, but that the fade is starting at the wrong opacity. If I do the following steps:
1) Create a sprite, add fade behaviour and set "Active at start" to false.
2) "On Spacebar down", set opacity to 50
3) Start fade.
Instead of the sprite starting at 50 and moving down to 0, it goes back to 100 (the default opacity) and then starts fading to 0. The reason being that it's basing the start opacity on maxOpacity, which gets set when the layout starts (not the new opacity I set in the action).