This is a long-standing design problem with the LabKey query APIs. The problem is that anytime you use a query you really have two components. a) the query/table b) the view over the query.

Unfortunately, these two parts don't cooperate very well, and the view definition's sort order will over ride the "ORDER BY" in the sql. In the first case since there's only one column the view is choosing to sort using it and it looks like the "ORDER BY" is working.

The solution is to use the separate "config.sort" property of the API call. We should add better documentation for this with our SQL reference.

Matt