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I am not sure if it will work in Presenter 5 .I can suggest you something that you can try .After publishing copy your flv to published folder resources/data folder in case of slide/sidebar swf respectively . :)
The reason why you can preview your content while in Slide Show mode in PowerPoint is because the reference to the inserted Captivate swf is still recognized as a locally run file. Once published, however, things change dramatically.
Although I'm not entirely sure how you developed/created your slidelets in Captivate, you can absolutely integrate your Captivate content within Presenter 5. In addition to Leo's advice, I'd like to weigh in on this, and in addition, I also wrote a 2 part article on my forum about integrating Captivate content containing Full Motion Recordings (similar to your situation)--this came after having the opportunity to talk with Silke Fleischer, Product Manager for Captivate.
Those articles can be found here:
Bottom line, when you add a Captivate swf using Presenter's Insert--Flash function, the inserted movie (assuming that you inserted the "base" swf file) can no longer "communicate" with the other swfs (including the flv that your Captivate project used) that were created during Captivate's publishing process. That usually results in "blank spots" during the playback of a Captivate movie where your flv should have appeared in your Presenter content.
So what's the fix? Actually, there are 2 that come to mind immediately.
1. Before publishing in Captivate, make sure you turn borders off which will eliminate the "_skin.swf" file. That'll be one less file to deal with.
2. As soon as you publish your PowerPoint deck, as Leo mentioned, go to the data directory and open up the resources folder. Within that folder, what you need to do is copy/paste all flv files from the published Captivate project.
Why? Because of how publishing works in Presenter. Each swf file you add using the Insert--Flash method ultimately results in swfs that are stored in the resources directory. And since Captivate uses dynamic loading to launch the FLV's at run-time, having everything in the same location means that the "base" swf file will be able to accurately call, and load, the FLV's appropriately. As an example, I set up a sample project here that uses Full Motion Recordings (instead of FLVs):
However, this assumes that can publish your Presenter content locally. And even IF you had to publish to a Connect server, you could always publish locally first, add the FLV into the resources directory, then zip the entire course and post on Connect or some other LMS.
Anyway, just my 2 cents....