Flash will not publish/export + FLV question

Hello,
I am currently building a game in Flash CS4, but am stuck due to a Flash problem.

The Problem:
Adobe Flash will not export, or publish my .FLA file, nor will it create a .SWF at the chosen destination under the publish settings. Whenever I try to export/publish my .FLA, the export/publish pop-up window opens, and the progress bar runs all the way through. Once that is done, the window which normally appears immediately afterward, in order to test the flash, does not appear.

Furthermore, Flash seems to have deleted the .SWF, and any other files I wish to publish the moment the publish/export process is completed. I have also found that I was unable to import files after this problem occurs (I select it in the menu, or hit the shortcut keys, but no window appears).

The strange thing about this problem is that I may be lucky and have Flash actually export and publish correctly on its first go. However, when I try again, it won’t publish/export until I restart flash.

This problem happened on three separate windows machines (Vista and 7) under both Flash CS4 and CS5.

Note:
I have discovered that this problem may be related to the many embedded FLV video clips I have created for the game’s character animations (6+ characters with 30 very short animations each).
These animations were rendered in a 3D CG software, which were then edited in Adobe After Effects, and exported as .FLVs for use in Flash.
Strangely, once I’ve deleted all the embedded FLV clips from the library, Flash will once again publish and export. This is not an acceptable solution to my problem, however. I already searched for any corrupted FLV files, but could not find any.

My questions are:
1. What can I do to make Flash publish/export once again, while having my embedded .FLV clips within the library? Is there something I am over-looking, or any settings I must change in Flash?

2. Which settings (in Adobe After Effects) are best to export .FLVs for use in flash?

3. If I cannot use FLVs, what other options do I have, in order to use my CG animations in Flash? I tried PNG sequences, but Flash complains about low memory, and crashes (FLVs were working great up until now).

Any help would be greatly appreciated. Thank you in advance.