Michael, the issues certainly sound strange and shouldn’t be happening. Just a couple of observations to think about. When you copy and paste a set of tasks, Project places them as subtasks of the previous task. That doesn’t seem to be the issue as you state it works after you close and reopen the schedule. Do you know what was used to develop contractor schedules? Was it a recent version of Microsoft Project or was it a different tool like P6. Is your Project current on it’s updates. Last question, is this something others are experiencing?
My first thought is to uninstall the software and reinstall. Download the software and install directly on your machine and not through a software management solution. Another thought would be to download a free 30 day trial of Project Pro for Office 365. This is the exact same software as you would install directly. The only difference is that it is a subscription solution instead of a purchase price.
In short what you are experiences is out of norm and shouldn’t be happening. Good luck and let me know if you can get it fixed.