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To your first question of animation not pausing when the slide pauses is the expected behavior.
The animation object timing and slide timing are independent of each other.
If you are using Captivate 5 version, then the animation can be made to pause along with the slide by adding animation as slide background. (Animation Slide)
On resuming the slide, the animation should not turn out grey unless it has some grey colour!!
Is it possible to share the animation? you can e-mail to my e-mail address firstname.lastname@example.org.
It was not the embedded animation that turned gray but the whole slide!
Since the original animation was from Captivate, we just copied the slides instead of trying to embed the swf. Our immediate needs are thus fulfilled. However, in the future, we will try the animation as a slide background if we need to do something similar.
(Unfortunately, I cannot share the animation because of corporate policy.)
Note: The question has not been answered but I marked it as answered because I no longer need an answer.
Embedding Captivate SWF' into another CP-file is not always working well. Just want to recommend a widget developed by Michael Lund, in a AS2 and a AS3 version. If you are using this workflow a lot, could be interesting. Have a look: