If you're using Maya 2016, you might already realize this. In Maya 2016, there's a new evaluation mechanism [knowledge.autodesk.com]. The default “Evaluation Mode” is “Parallel”. However, this doesn't work with the Houdini Engine plugin at the moment, so the asset won't be dirtied and updated properly. Fortunately, they still support the old evaluation mode, so you can work around the problem by switching the “Evaluation Mode” back to “DG”.
I need to look into how the plugin can be adjusted to work under this new mechanism. Hopefully, this won't be too major of a change.