If I use the new-to-1.8.1 Rebuild Index feature, with a single message selected, once the operation is complete there is no selection; however, the message pane continues to show the message that was selected. If a multiple selection beforehand, then the only symptom is the selection is lost. My preferred behavior is to maintain the selection (as in bug 362241); if that's not feasible or too much work, then at least the message pane should be cleared (like in bug 192870). I see this in TB and SM, branch and trunk.

Are there any error messages in Error Console(Javascript console)? See Bug 355194.

Yes, as a matter of fact -- this from TB 2.0 final: Error: uncaught exception: [Exception... "Component returned failure code: 0xc1f30001 (NS_ERROR_NOT_INITIALIZED) [nsIMsgFolder.updateFolder]" nsresult: "0xc1f30001 (NS_ERROR_NOT_INITIALIZED)" location: "JS frame :: chrome://messenger/content/widgetglue.js :: RebuildSummaryFile :: line 249" data: no] Similar seen in trunk, as per 355194. Don't know if solving that would necessarily fix this, however.