Some changes were implemented yesterday to help resolve the metadata issues when executing Tophat. At this time, most of the datasets will not report this problem, but one still will (accepted hits) for certain jobs. For this output, when this occurs, using the reset metadata link in the yellow box for the dataset should correct the problem.
Our team is continuing to work to resolve the issue fully, but there is no firm timeline for completion (yet).
Thanks again for reporting the problem, Jen, Galaxy team