Consider this scenario. You have a ClickOnce application that always succeeds when first installed. However during subsequent launches the ClickOnce application fails while checking for updates. It appears to be random, but more prevalent when there is an update available.
Another way to determine if this article applies is if the problem is corrected even temporarily by deleting the ClickOnce File Cache. See the More Information section.
Anything that interrupts the synchronization between the file system and the registry data can cause a ClickOnce application update to fail.
An incomplete System Restore that restores only the files but not the user profile. The registry key HKEY_CURRENT_USER\Software\Classes\Software\Microsoft\Windows\CurrentVersion\Deployment\SideBySide\2.0 should be in the same state as the files in the following folders
Ungraceful operating system shutdowns such as a power failure.
Ungraceful log off such as powering off machine rather than logging off or shutting down.
Besides avoiding the scenarios listed in the Cause section some reduction on corruption can be seen by using framework 4.0 or higher on the target machines. Framework 4.0 has improvements that make it more robust resulting in fewer update failures compared to the earlier framework versions. The application does not have to be developed using the framework 4.0. It just needs to be installed on the target machines.
Microsoft continues to look into these failures and will update this article as new information becomes available. The mitigation for these issues continues to be
Attempt to uninstall the application from Add and Remove Programs (ARP, Windows XP) or Programs and Features (Windows Vista and later operating systems).
If the program does not uninstall successfully, see the More Information section on deleting the ClickOnce File Cache.
If you would like to submit information for such a failing ClickOnce deployment
Verify the issue matches the symtoms listed in this article.
Submit a Connect bug. (Microsoft Support will not handle this particular issue. The Microsoft ClickOnce Product Team will address the Connect bugs). See the More Information section for the Connect bug portal.
To delete the ClickOnce file cache delete the contents of this folder based on the operating system.
Windows XP and Server 2003 - %userprofile%\Local Settings\Apps\2.0\*.* Windows Vista and Server 2008 and later - %userprofile%\AppData\Local\Apps\2.0\*.*
Deleting these files will clear the information for all installed ClickOnce applications. They will re-install the next time their shortcut or URLs are used.
It is not necessary to delete the registry data. For reference the ClickOnce registry data is located in HKEY_CURRENT_USER\Software\Classes\Software\Microsoft\Windows\CurrentVersion\Deployment\SideBySide\2.0.
The Connect Portal is https://connect.microsoft.com/. When submitting a bug for this issue include the error log. Attach the registry export and ClickOnce file cache.
Include ClickOnce Store Corruption in your bug title.
Microsoft .NET Framework 1.1 Service Pack 1, Microsoft .NET Framework 2.0, Microsoft .NET Framework 2.0 Service Pack 2, Microsoft .NET Framework 3.0 Service Pack 2, Microsoft .NET Framework 3.5 Service Pack 1, Microsoft .NET Framework 3.5.1, Microsoft .NET Framework 4