I have a workaround for this, but it’s a very tedious way of keeping your videos in sync.
I wait until I have a reasonable sized batch of new videos to add to my library. Once added I shutdown the box and disconnect it from the internet. I then download the old (working) firmware onto the root directory of a USB stick. Use this link for the previous firmware: http://dl.boxee.tv/version/dlink.dsm380/184.108.40.20650/boxee.iso
Boot up the box into service mode by keeping the power button pressed down for around 10 seconds, then when in the service mode menu put in the USB stick and wait a couple of seconds for it to be recognised. Then select Upgrade from USB. The old firmware will then be installed.
Once fully installed and booted back into boxee you can then go in and manually adjust each of your newly added videos to their desired audio delay settings.
After you have finished this process you are free to connect the box back to the internet again and the newest firmware will begin to automatically download. Update back to the newest firmware and the audio delay times which you just inputted will be remembered and your new videos will now all play correctly on the current firmware.
Obviously this is a crazy and very convoluted way of getting past this problem, but it’s the only solution I can think of until they return this functionality back to us.