Joe,
thanks for your very thoughtful comments and test report.
WP Clone fails on larger sites (up to 250mb is generally safe however) and on poor-quality hosts (specifically, Godaddy standard hosting, i have no tested on new godaddy cpanel hosting). Jetpack is a very large plugin (1mb) however I don't think this should take the backup size over the limit. So I am not sure what may be causing the problem. Our developer is currently sick (we are a training company not really a development company) and will have him test the plugin with Jetpack and report back here. I suspect however the problem is not caused by Jetpack but by one of the two reasons above.
For anybody else reading this post, try the Duplicator plugin which seems reliable but not as fast as WP Clone and also requires FTP
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WP Academy on "Does not work with Jetpack"
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