I run a project called flXHR ( http://flxhr.flensed.com ) which is a flash proxy for client side, cross-domain Ajax calls. When I tried to open my flXHR.swf file with your tool, it complains about malformed headers and not being able to open it.
However, this SWF works just fine, it's used all over the place on my site and by others. What's wrong?
HP SWFScan has certain controls in place that allows it to identify malicious/malformed SWFs. In case of "flXHR.swf", the tool could not successfully validate the SWF header format and hence delivered the error message: "Malformed data in SWF Header". Since the header could not be validated, the SWF was not decompiled.
One suggestion would be to reduce the frame size of the SWF and try decompiling again.