Unfortunately there is no setting or code that will guarantee that the documents will be in order in IndexPlus. It depends on the details of the structure of the process, processing environment, what has occurred previously with the batch processing, the number of modules processing a particular task, and other details.
For example, suppose a batch is scanned in that has 20 pages/documents. Then in the next step in the process is Image Enhancement, and there are 2 instances of IE running on different machines to handle the volume of tasks that it needs to process. Some of the tasks go to 1 machine for processing and some of the tasks go to the other machine. One client has a more powerful processor than the other and faster network card so these tasks are processed faster than on the other machine. The tasks are sent to client in FIFO, first in first out, order by priority. So if all of the task had the same priority and IndexPlus was the next step in the process, the task wouldn’t necessarily be in the order they were scanned. If page one went to the machine with the slower processor and network card, it would possible get triggered at IndexPlus after page number 2 which was processed by the faster machine. Not saying this is your issue but there a lot of ways batches will not be triggered in order. If you open a task and then close it, it goes to the bottom of the pile for processing and will be send to client after all those in front on it. Again there are other reasons why they may not be in order as well. The process that keeps them in order may be much simpler than the one that mixes then up.
Hope this helps.