not able to use custom queries

Hi, we use the free “Post Types Order” plugin. I have turned off the auto sort function because it was causing issues with some queries (i.e. not showing the latest posts first but adding them in random spots). So, instead I want to use custom queries (ordering posts by date) on some pages. However, my custom queries aren’t respected, no matter what I’m trying to order posts by. I also tried hiding the post order interface for standard WordPress posts but that didn’t help. (We only need custom post orders for a custom post type.) Is there a code snippet I can add that forces custom queries to be respected when auto sort is turned off? Thanks