Are you able to show us a graphic or mockup of what you wanted? It's a little difficult to envisage your idea just from the description so far.
For example, I'd Like my presentation to start with the word
(In dutch) and after a while (audio in the background with explanation) the 't' appears in red:
And while an audio is playing the t sometimes blinks, or grows bigger, or changes color, gets underlined, etc.
This can also happen in the middle of the word, like in
where also the t needs to blink or highlight at certain moments in the presentation.
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OK. I think I get the idea. I doubt that Captivate will be the right tool for your task. I'm not saying it would be impossible, just that there are other tools out there (like Flash) that would offer you a greater level of control, albeit with a steeper learning curve.
In Captivate you can only animate or apply effects similar to what you describe on individual objects. So to use an Effect to animate or change the colour of something, but if you wanted to do this to an individual letter in a word, then each letter would need to be in a separate text caption or be a separate graphic.
There are lots of easier ways to make something stand out. If I had to teach language words, and I wanted to highlight a given letter in the word using Captivate, I'd probably make the words quite large, then use a Highlight Box placed over the letter and either use a border or set to Fill Outer Area with about 50% Alpha so that only the letter in the highlight box could be easily read.