I did find the solution on my own.

FCKeditor does not recognize the flash files if they haven't been uploaded through it's interface it seems. Since when I uploaded the files to the same folder where I had put them manually before all worked just fine. Though one have to set the width and height manually and remove the paragraph tags before it works ok.

And those p tags really are annoying in that editor since they totally mess up the site layout. And I am pretty sure that there will be complaints from the ones that will do the site management. Though that is a later problem., and a solution is to craft modules for combined flash/image insertion that dont add stupid not wanted things. But that is a later issue