Can you anyone explain to me why calendar invitations do not appear in the invitations sidebar?

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It depends on your server - notifications show in Sidebar only If your server does support Automatic Scheduling. Otherwise, they come only as email.

The server is Google Apps does this support automatic scheduling.

Yes, Automatic scheduling should be supported on Google Apps. If the invitations still do not show in Sidebar, enable GData logging and simulate the issue. Then send us the logs using the same window. Thank you.