It sounds like a bug to me. It should retain the url parameters.
The <?php echo($assumedRoot); ?> stores two values so that you can have a different structure on your testing server and don't need to update the menu to go live.
You can remove it by hand, but I don't think that has anything to do with the problem reported.
Not retaining URL parameters is a bug if it happens. Support is pretty responsive and that is the best route to getting bugs looked into and resolved by an engineer. It can take longer if the problem is a bug or is unreproduceable simply because those things take more time to look into.