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If it is a movieclip symbol (or a graphic symbol) you can tween the alpha value between keyframes using a motion tween. I would use a classic tween because I have not used the newer one. If this is not working for you then chances are you are not setting things up correctly.
I have just tried some experiments.
1) Create a white box for 1st KF, make it an MC, create a second KF 3 secs later, make this one alpha 1% then make 1st KF's MC alpha 100%. Create a classic tween by right clicking between the two, scrub the timeline slider and hey presto fade of alpha :-)
2) Ditto but this time use one of the white spatter png's instead of the white box, scrub and bingo png fades.
Now lets look at my MC that I am wishing to fade from 21% to 1%.
Double click it in the Lib and we see it is 5 frames long, each is a KF and each KF has a different png file allocated to it (drag drop from lib to MC stage). Each png is white pixels in a spatter pattern sitting on a transparent base. Each png is a larger spatter than the last, thats 5 separate png files with unique names created in photoshop. So the spatter gets larger as the MovieClip plays, it plays spatter1.png then next frame spatter2.png then spatter3.png etc, very quickly in fact and it loops (no stop command), I could have gone 1 2 3 4 5 4 3 2 so the growth developed then shrank but it looks ok for my purposes with 1 2 3 4 5 as its so fast.
It is one of those png's that was used in experiment 2. It worked there, so alpha applied to png works.
When we have five of them in the MC that we are fading, or trying to, we have failure.
...update...sussed it !
I had placed the MC in 1st KF, copy pasted it in place and moved it upwards to get two of them sitting parallel, then created the next KF 3 secs later, made the first two in 1st KF 21%, made the last two 1%, classic tweened and got failure.
Now trying only 1 per Classic Tween and using two layers, one for the lower, the other for the upper, it works.
Lesson learnt, you cannot have two MC's on one layer if tweening in this way. Its got to be one MC tween per layer.
When tweening on the timeline you can only have one object involved and that object has to be the same object from the first to the last keyframe.
Shape tweening you can have different shapes objects but Classic Tweening the same MC.