If the Zephyr DCS50 repeatedly shuts down briefly and then comes back on again, it is probably being run too close to its pre-set current limit of 2.5 Amps or it may be overheating due to restricted air flow to the bottom of the unit. In this case it may clip or mutilate some outgoing packets of information to keep the track current within acceptable limits.
To solve this problem, reduce the track current load by running fewer locomotives or setting up additional power districts and adding more boosters to provide more power for the layout. With more sound decoder equipped locomotives, this is more likely to be a problem. If the DCS50 is completely enclosed, either add a fan or install it in a better ventialted location.