The last few platform updates have changed CSS a lot, and this will continue for version 1.1. When you upgrade to a new version of the JS file, you must also repackage your theme from Themeroller.
In the latest update, they slightly changed the CSS structure for fixed headers and footers, transitions, and some other things (for example, the download update was updated). The latest update also gave the boot message more options, so the HTML structure probably changed and the old CSS is not quite right compared to the new JS.
To verify this, you can reference the standard current version of CSS and see if the download message is displayed correctly.
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