I've used http://nowrap.de/flare.html in the past to good effect for v1 and v2, and while I have not touched it since my SEC542 class, the OWASP project SWFIntruder may be a good option as well. It's a run-time analysis tool designed for security.

https://www.owasp.org/index.php/Category:SWFIntruder

It's also possible that the HP tool is not working because protection mechanisms like http://www.dcomsoft.com/ http://www.kindi.com/swf-encryption.php http://www.amayeta.com/software/swfencrypt/ (as well as many other examples) have been used to prevent it.

There's no guarantee that commercial tools will help here if such methods have been employed.

You may find some other alternatives at http://www.swftools.com/tools-category.php?cat=759

I know one of my developers has used this site for some freeware utilities but I have no direct experience myself.

So did Sothink work for you? I'm curious because I may have to take a look at it for my own toolset.

Yeah Flare does not support v3 at all. It's somewhat dated and has not been updated in awhile but it works great for v1 and v2. SwfIntruder is used for runtime analysis, I don't know that it will decompiler a swf but it will provide you much of the same information you'd be looking for in a decompiler with the added benefit of doing several security checks on the analyzed swf. It does support v3 as far as I know. I really don't understand why the HP tool would not work. Would you mind linking to the sample files you are discussing? I'm interested to see whats going on here.