Ok, first I would reccomend you update to 7.0.6 through the Adobe Updater or 7.0.7 through the download avaialble at http://www.adobe.com/products/presenter/.
As to your issue of importing the flash file, if you are using Captivate 5 or 5.5 it publishes to AS3 (Action Script 3) only, and presenter 7.0.0-7.0.6 is an AS2 application. Therefore your Captivate SWF files will not work in Presenter. So if you are using Captivate 5 or newer, you must go to Presenter 7.0.7 for the SWF files to work.
The problem you describe sounds to me like you are working on a PPT file that is on a shared drive. Presenter doesn't like working with files that are not on your computer, and will tend to not show the dialogs for inserting Flash, Videos, or Audio if the presenation is on a shared drive.
Thanks, Jorma. I moved the PPT file to my machine and now I get the dialog window to select the swf file.
I am still having an audio problem (my narration, recorded in Captivate, is gone and all I hear is the mouse-click noise that Presenter generates) but I imagine I'll be able to figure that one out. I have not yet upgraded to 7.0.7.
btw: I'm using Captivate 3.
Glad that we got 80% of the way there.
The audio and mouse clicks are in Captivate (Presenter doesn't generate mouse clicks). Double check in your Preferences in Captivate that the box to publish audio is checked, just incase.