I ran into this little problem when I noticed importing a flash file into presenter only takes the root swf, and does not handle any external resources that swf may need.
For instance if you have a captivate demo, some of those full motion recordings may not show when you import that demo into presenter!
Not very helpful is it!
Worry not, this is a simple copy and paste solution. First do your import into Adobe Presenter and publish. Then copy any other swf file that the imported flash object is going to need and paste it into the /data/resources folder found from your published presentation file.
If you want something done right, sometimes you gotta do it yourself I guess!