Try each of the following steps in order until the issue is resolved:

1. If working with particularly large queries, please be patient and allow The Raiser's Edge time to complete the merge.  Large merges can sometimes take more than a few minutes.
2. Recreate the merge.
3. If this happens for a specific user, add a new user name with the same security rights as the problem user.
4. If this corrects the issue, review What to consider before deleting a user name and delete the problem user name.