As I understand it QuickBooks must not be running to synchronize multiple companies. We have a a schedule to synch QQube at 2am on a Terminal Server with multiple users but it fails because someone forgets to exit QuickBooks. Is there a way to automatically exit QuickBooks at 10pm for all users?
No there isn't. But it shouldn't matter. QQube logs into automatically to the users you created, and in multi-user mode - so as not to affect anybody else logged in.
On a Terminal Services environment, there are specific instructions for installation. Were you able to follow those? https://clearify.com/wiki/view/278/multi-user-remote-desktop-environment In that environment, if the installation is not properly followed to the letter, you will get a situation, such as you mention.
Another possibility, is that you have QuickStart Enabled in QB the Synch Session (it is not a global setting, but a specific user setting). This and error code 800408, are common issues, but controllable: https://clearify.com/wiki/view/381/error-80040408-quickbooks-doesn-t-start
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