In accordance with security update warning on admin/reports/status and admin/reports/updates I have just upgraded a number of sites and subsites on various servers to Drupal-6.28 and also upgraded all indicated contributed modules, including the Zen theme (which I leverage for custom themes), from Zen 6.x-1.0-beta3 to Recommended version: 6.x-1.2.
On some (only) of the sites thereafter the admin/reports/updates page still claims the theme Zen 6.x-1.0-beta3 is present and 'Security update required!', although clearly Zen 6.x-1.2 is installed, and it is listed ok on the themes listing page. I have tried clearing all caches, including theme registry and running cron but still admin/reports/updates stubbornly insists the older Zen version is present. but only on the Available updates page, and the Status report page still claims 'There are security updates available for one or more of your modules or themes.'
In each sub-site case the new zen is installed according to this pattern (and the old zen has been completely removed):
.../sites/www.subsite.com/themes/zen
.../sites/www.subsite.com/themes/mysubsitetheme
The problem does not occur for the default site where zen is explicitly installed at:
.../sites/default/themes/zen
.../sites/default/themes/mytheme
I do not have any themes under /sites/all.