We try to be pretty good about setting the right capability bits, but sometimes this just don't work out right. For example, if you set a Group node as the key to the map with ALLOW_CHILDREN_WRITE, and we're using a TransformGroup as the internal implementation, then we won't pick that up: our code uses TransformGroup.class as the key to the map. There's a lot of places where this comes into play due to all the derived classes that are part of the Java3D design.
If you have specific instances that are not being set correctly, please post a bug report at http://bugzilla.xj3d.org
for us to look through. Sometimes these are just trivial errors in our handling and can be fixed in a minute or too. Doing a generic audit is something we currently don't have time to do, but if we know of specific cases, that makes our lives much, much easier and we can take the hour or two out of our schedule to go fix it.