WordPress MU Sitewide Tags Pages has been updated. In the latest version:
+= 0.4.1.1 =
+* Run populate feature in source blog context.
+* Added resource warning for populate feature.
+* Fixed PHP warnings.
+* Only insert categories for published posts.
If you noticed in WordPress 3.1.3 that posts were being duplicated, this fixes it. Thanks for those who helped work through this issue in these threads.