(Apologies that I don't have a convenient reproduction of this problem, I'm working with private code that I cannot share.)

The ui-helper-hidden-accessible class specifies position:absolute. When this applies to a checkbox <input>, Chrome suffers from what appears to be a long-standing side-effect, as described in this ancient StackOverflow question: If the checkbox is contained in a bunch of nested <div>s where one of the ancestors is vertically scrolled, when the checkbox is clicked the scrolled ancestor's top/y value is adjusted by the scrolled amount, causing the <div> to become clipped at the top. If there's enough scrolling, the <div> can disappear entirely.

This does not happen in Firefox.

To work around this, I set position:fixed explicitly on the checkbox <input>, overriding ui-helper-hidden-accessible's value.

I think jQueryUI should address this problem. I'm not sure if it's OK to change ui-helper-hidden-accessible's value for position, or if it should only be done for checkbox <input>s (or if there's a better way to deal with this).