The Devs are aware of it and are researching the issue. You can find more info in the publishing Broken
thread under the Search of "Foundry Publishing".
I almost did a republish myself, but found out just in time by a Fleetmate who had the problem too.
If I run a mission that bugs I will not downrate it. I usually like to send a PM to the author
to let them know. If it a mission stopper, I will drop it and rerun it when it is fixed. It is not fair
and it is frustrating to all of us authors when there is a bug that we cannot control
infesting our missions causing us to get a 1 star rating with the comment "Mission is Broken".
Hopefully it will be fixed soon so we can continue to use the awesome abilities the Foundry offers us.
Omega Directive Revisited (Part I - The Investigation) - Not precise Trek canon
Omega Directive Revisited II (Part II - Break the Link) -Strong Trek canon.