I missed this one in my search, so I created the duplicate issue. However, I have experienced the same problem.
It only occurs when you create multiple aliases using a with clause. If you happen to add those aliases in the same order as the internal Hibernate listing of properties, then the parameters are added in the correct order.

The basic problem is that the values are added in the order that they are added to the criteria, but the joins are created based on the internal cache of properties. For single class, annotated POJOs, this is the order in which the properties are enumerated in the POJO, but for more complicated entities, that may not be the case.