Thanks for stopping by our humble corner of Internet ADFS knowledge sharing. :)
Have you guys done interop verification with Microsoft on ADFS V1? If this was a common problem with ADFS, I would have expected this to show up then, so perhaps this is a more subtle defect?
This sounds to me like a low level XML DSig issue that is probably related to some sort of canonicalization issue. I would not be surprised if the problem was somewhere in the .NET XML core and not actually related to the ADFS code base itself since it uses the underlying .NET core stuff for dsig. I also would not be surprised that this type of issue might generate an argument as to whose problem it was. :)
That said, there appears to be some sort of a problem here that needs to be figured out.
I can try to put you in touch with my contacts at Microsoft to examine the issue if that would be helpful. I don't work there, but I do have some friends on the product team. FWIw, I know they are excited about your project because I once asked one of their lead architects for recommendations on clean, inexpensive options for Java-based shops looking to support WS-Fed PRP and they recommended OpenSSO to me. I've repeated this advice several times to some of my business partners, although I don't think any of my company's current partners are using it yet.