I have test it with Visual Studio 2008 RTM, it works well now. The following steps are my test procedures.
1. Create a solution with two Windows Application projects, WinAppA and WinAppB.
2. Set WinAppA as publish project and add a reference to the WinAppB.
3. Open WinAppB properties window.
4. Click Signing tab, sign the ClickOnce manifests.
5. Click Security tab, enable the ClickOnce security settings.
6. Publish the WinAppA, publish well.
7. Test published WinAppA, it works well.