I'm facing a strange issue after upgrading from 6.x-1.0-beta5 to 6.x-1.0-rc1. Follow these steps to reproduce :

1. install Vertical Tabs 6.x-1.0-beta5 and tabify some fields for some content types
2. update Vertical Tabs to 6.x-1.0-rc1
3. go to admin/setting/vertical-tabs and check "Expose vertical tabs selection on the edit content type forms."
4. go edit a node: the tab selection you've done in 1. is gone, fields do not display as expected
5. go to admin/content/node-type/[your content type]: you can see, under Vertical Tabs, that your settings are however correct
6. save the content-type form
7. go back editing some node: the tab selection is now correct

Both in 1.0-beta5 and 1.0-rc1, per content-type settings seems stored in the vertical_tabs_forms variable. After looking at the code, I don't understand why the settings are loaded correctly on the content-type forms, and why we have to save every content type form for the settings to be taken into account on the node edit forms.