When creating new tasks in Microsoft Project (MSP), after saving the file back to PPM and re-exporting to MSP, the tasks move to the bottom of the project (or bottom of the summary task if added under a phase/summary task). Symptoms can also be seen if clicking F9 to update the MSP scree, where tasks will then end up out of order. 

Steps to Reproduce:

1. Create a new project in PPM and add a 4 new tasks to the project 
2. Export the project to MSP
3. Insert a new task "Task 5" in between Task 2 and Task 3 so that it shows up as the third task in the plan
4. Save the project back to PPM
5. Export the project back to MSP

Expected Results: The tasks remain in the same order (Task 5 displays in between Task 2 and Task 3)
Actual Results: The newly created task (Task 5) shows up at the bottom of the project 

This is due to a setting in Microsoft Project

This applies to all supported PAS environments for all releases.

1. Open a project that has the issue (or a new project) 
2. Click on the 'View' tab in MSP 
3. Click on the 'Sort' option from the menu then select 'Sort By...' 
4. Change Sort by from 'Unique ID' (if showing for you) to 'ID' 
5. Uncheck the box titled 'Permanently renumber tasks' 
6. Click 'Sort' 
7. Save the current view to the Global.MPT:

• For custom views:
  • Go to the View tab
  • Click on one of the Views drop down (such as "Gantt Chart")
  • Click "Save View",  select the radio option for 'Update Current View' then click OK.
  • Click 'Yes" to the message prompt that asks if you want to replace the view in the Global.MPT
• For out of the box views (such as Gantt Chart): 
  • Go to File->Organizer 
  • Click on the View under the right hand column and click Copy to move it to the Global.MPT column 
  • Click 'Yes" to the message prompt that asks if you want to replace the view in the Global.MPT

Reference KB000071385 - CA PPM and MSP integration - List of Knowledge Documents
Reference KB000015956 - CA PPM and MSP integration known defects - Support Technical Document Index