I have noticed something a bit strange, and am not quite sure how to fix it, although its not mission critical but more of an annoyance.
So what happens is the h264 encoder filter is used within an application but if copied to a new machine, say to intall that application... the filter does not work the first time. I've found that opening graphedit... pulling in the filter... and then loading the property pages does something and there after the application can then utilize the filter.
Not sure what the issue may be. There should be no issue doing what you describe. The filter does not depend on a specific registry entry. If the is no filter registry entry, it will be created when first executing the filter.
Was the correct filter registered successfully on the new system before running the application?
Can you provide some more info on what happens "when it does not work". Do you get an error message?