I'm using an instance of Popup. It contains an HtmlContainer and a few other widgets. Many of the widgets, including the HtmlContainer, allow the mouse events to propagate to the container under the popup.
I did some further experimenting, and found the same problem with the popup list of a ComboBox. Here's what I did:
For my primary application container I used a BorderLayout, with only a west and center panel. In the west panel I added a ComboBox that spans the width of the west panel. Then I click the dropdown button. The border layout splitter is situated under the combobox dropdown list. So now when I move the mouse over the entries in the dropdown list, if the mouse position corresponds to the position of the underlying splitter in my main panel, the mouse cursor changes and I can actually manipulate the splitter.
I've also found that once I've changed the splitter position in my main panel, subsequent use of the combobox no longer exhibits this behavior.