We had the same issue on our build server. MsTest seemed to remove DLLs it deemed unnecessary (note : this claim is only an educated guess). To fix it, add an explicit call to something in AutoMapper.Net4.dll. For instance, with the class ListSourceMapper :
var useless = new ListSourceMapper()
Adding this to a project which is shared by all other projects fixed it for us. Where to put this line of code may vary.