Save/export PS animation as video; transparent areas always render as black?

Question

Hello all,
Thank you in advance for taking the time with this; I'm sure there's a very simple solution to this problem, and I've scoured all the help files and forums, and tried the suggestions, to no avail. Please help?
Here's the problem;
I've created an animation in PS CS5, 139 frames, of a logo on transparent background. The colours (24 bit) within the logo change gradually during the animation. Each layer has transparent background, and I've saved an Alpha channel as well.
I want to save it as a video, so that I can use it in an interactive presentation that I want to create in InDesign.
Can't do it as an animated Gif; 256 colours dithered, don't look good, so I'm trying to export it as video (Quicktime) (-but if alternative is better, will try that!).
No matter what options I try, the transparent background always ends up as solid black in the video, either when played in QT Player, or when I convert it (with Media Encoder) to FLVorF4V and import it into InDesign. (InDesign seems unable to import Quicktime directly?)
...but I need the background transparent!?.
Amongst the many ways I've tried, I've tried the 'Help' recommended method:
"Render Video>Quicktime Export: Quicktime Movie> Settings: Animation / Millions of Colors+ / Quality=best, with Render options: straight unmatted
(& I tried all other options here).
-but no luck.
I've read that InDesign can read PS files, so tried that as well, but only first frame comes in (or is it flattened?) either way, no layers.
Maybe it's my ignorance of CS5; I've been using Photoshop since it was born, but stuck at CS2 for past few years; CS5 is significantly different, and I'm new to video!.
...and am (trying) to learn InDesign & others in the CS5 suite.
Please (if you have the time) can anyone give me a step-by-step, total idiots' guide to the procedure; I just know I'm misunderstanding something, or just not getting someting that I should be doing.
-Whether I need to set up the PS file differently, or the animation pane, or the export video options differently, (or importing into InDesign) ...I'm at a loss.
Sorry, I'm new to threads, so don't know how else to include/post specs., so here they are:
PC machine,
Q9550 Intel processor, 8gb Ram,
terabytes of disk space,
dual monitors,
Win XP SP3/Win7 dual boot (but using win xp for this),
CS5 Design premium suite, latest updates installed.
(pls. tell me if you need any more info?)
...All this kit and I can't achieve this simple task!!
I might be out later, so please don't think I'm rude if I don't reply immediately to any respondents; I will get back as soon as possible, I do need to solve this, and very much appreciate any help offered.
Many thanks!

Answer 1

Hi Noel,
Thanks for your interest, sorry about the delay in me replying; I had to go out.
To answer your questions, perhaps if I describe the way I want to use it in Indesign?
The logo is a hard edged shape, in which colours smoothly and continuously change/animate, which is why I need it to be video, rather than a static image, eg. tiff/png which of course would be simple.
The area around the logo needs to be transparent, as I want to be able to move it around on screen, over changing backgrounds, pictures and graphics (that are themselves animated within InDesign, using motion paths etc.).
I don't want a black or white rectangle to be around the logo, as this would obscure some of what's behind it.
I know this (the logo with transparent background) can (somehow!) be done as a flash video, as similar stuff is used on the web all the time.
For instance, little smiley-faces or graphics (or video!) that bounce up and down in web pages to get your attention; they're usually animated gifs or flash, and they don't have black or white rectangle containing the shape. Not a great example, but you get what I mean?
Does this explain better what I'd like to achieve?
Indesign does provide guidance; it says to import flash videos with an alpha channel (for the transparency)...which is what I've been trying to do!!!
I created the animation in photoshop, but photoshop can't export to flash.
So I have to export to Quicktime movie, then convert that to flash, using the Adobe Media Encoder program.
I think that's where the problem is happening; despite trying all and any of the options to do with alpha channels in this program, I still get black background around the logo video.   ????
Thank you for any help/advice you can offer!