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I wonder if a specific browser plugin could be to blame... messing with the DOM.

We are aware of these rogue blank lines appearing in the editor unwanted, but do not yet know how it happens.

In admin, Store Settings, Offline tab.

We need to find out why they aren't 'sticking'. My experience tells me to first look at those settings that could possibly make the aggregate amount of content larger than 64KiB. Those settings are the Offline Message and Copyright Text. Then second, look at the error log.

Yes, indeed. Please understand what is happening: In admin Store Settings, observe the various tabs across the top: General, Features, Layout, Stock, Search Engines, etc. These tabs drive a javascript function that causes the related panel of info to acquire the CSS property that makes that panel "visible". All other panels of content are not displayed. When clicking the Save button, all of the form elements on all of the panels of content - visible and not - get sent from the browser. So, even when you are only changing one or two settings, the web form is still sending all of the form's elements from all of the panels - because Store Settings is, in fact, one very long form that only a part of it is visible at a time. Your browser's Developer Tools, Network tab can show you the details of what was POSTed to your site.

For CubeCart not accepting any of the general store settings probably means that one or more of the admin-supplied data items is extraordinarily long. Settings that could get out-of-hand include a really long Offline Message, or a really long Copyright Text. All the data is probably getting sent from the browser to CubeCart, but then CubeCart wants to "serialize" all that data, and the limit is 64KiB. You might also want to create the error log to see if CubeCart is complaining about anything. https://forums.cubecart.com/topic/51550-how-to-create-the-error-log/

So there must be another cache. A content delivery network proxy or something typically used by cheap hosting providers. Does the basket reliably hold its contents between page loads?