I have hit this before, but it was VSTO related and posted about it http://jake.ginnivan.net/clickonce-deployment-in-teamcity

When trying to publish my clickonce installer I am getting the error:

[14:55:16]: [_DeploymentGenerateBootstrapper] GenerateBootstrapper
[14:55:16]: [GenerateBootstrapper] c:\Windows\Microsoft.NET\Framework\v4.0.30319\Microsoft.Common.targets(3939, 9): warning MSB3155: Item 'Microsoft.Windows.Installer.3.1' could not be located in 'C:\TeamCity\buildAgent\work\63190f273e745a25\TrainersAdmin'.
[14:55:16]: [GenerateBootstrapper] c:\Windows\Microsoft.NET\Framework\v4.0.30319\Microsoft.Common.targets(3939, 9): warning MSB3155: Item '.NETFramework,Version=v4.0' could not be located in 'C:\TeamCity\buildAgent\work\63190f273e745a25\TrainersAdmin'.
[14:55:16]: [GenerateBootstrapper] c:\Windows\Microsoft.NET\Framework\v4.0.30319\Microsoft.Common.targets(3939, 9): error MSB3147: Could not find required file 'setup.bin' in 'C:\TeamCity\buildAgent\work\63190f273e745a25\ProjectName\Engine'.

If your build server is a x64 operating system copy 'C:\Program Files (x86)\Microsoft SDKs\Windows\v7.0A\Bootstrapper\' to the same directory on the build server, then copy the blow code into a file called FixBootstrapper.reg, then run it.

Windows Registry Editor Version 5.00

[HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\GenericBootstrapper\4.0]
"Path"="C:\\Program Files (x86)\\Microsoft SDKs\\Windows\\v7.0A\\Bootstrapper\\"

If you have a x86 build server, upgrade. Otherwise copy ‘C:\Program Files\Microsoft SDKs\Windows\v7.0A\Bootstrapper\’ to the same directory, then copy the blow into a registry file

Windows Registry Editor Version 5.00

[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\GenericBootstrapper\4.0]
"Path"="C:\\Program Files\\Microsoft SDKs\\Windows\\v7.0A\\Bootstrapper\\"