I’ve just imported the file you’ve attached, and it imported all of the 11 layouts.The repeater subfields were also imported correctly.
It’s possible that your server has a post limit that causes that behaviour. Could you please try the fix on this page: http://www.advancedcustomfields.com/resources/limit-number-fields/?
Also, Could you please try to reproduce the issue on one of the WordPress’ stock themes (like Twenty Fifteen) with other plugins deactivated? If it disappears, then you can activate the theme and plugins one by one to see which one causes the issue.
Regarding the old layouts, It’s possible that you have a cache plugin or activated the Local JSON feature. Please clear your website cache and check if you have ACF Local JSON file in your installation.
I hope this helps.
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