This all used to work fine. Took me a while to track problem down to generic problem with your plugin's interaction with my theme (I suppose). Here's what I can say.
All performance of (recently updated to latest Pro version) works as expected. I can add and see all custom sidebars. Furthermore I can get these sidebars to appear on pages via the "sidebar locations" link, say for all posts of a given type.
All the sidebars also appear in the dropdown for the Custom Sidebar metabox, and these can be selected. When I update the post, however, the selection reverts to an empty entry (or the sidebar selected in the past).
And by this last comment, what I mean is that back when this all used to work, I had specified certain sidebars for certain pages, and now these pages are 'stuck' with that setting. New pages are 'stuck' on empty.
Hope that makes some sense. Any help debugging this would be greatly appreciated,