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I've been using MYOB Live checked in for quite a while and I checked it out last week and I have some questions.
Usually, the back up doesn't take long unless your file is really big and if you are online and your internet connection is not the best. With the second issue of the system reminder to backup can be activated from Setup >> Preferences >> Security >> select "Prompt for Data Backup When Closing". When this option is unticked it will not remind you as you are experiencing it now.
Hope this helps! Please let us know how you go as we are happy to help further.