I've had a ton of issues trying to get ClickOnce to work with MS Team Build starting from TFS 2005; we're now using TFS 2008. Getting a bootstrap package to work with TeamBuild took some work, but I was able to do it with success early on.
In our 2005 environment, I had to place the signing certificate that I was using onto our build server and place it in the certificate store in order for any of my builds to work. Without the stored certificate my builds would not complete. Fine, my bootstrap packages work, but my ClickOnce builds didn't. I didn't feel too bad because a ton of people out there have had issues with ClickOnce and Team Build.
Fast forward to our 2008 environment. I had some minor issues with my bootstrap package as I posted about when I started my blog, but nothing compared to the ClickOnce issues I've had. I decided to create a new build for my project in VS 2008 and start fresh. I still got the same result: my build would hang and return no warnings.
My coworker got ClickOnce automation working on his project and I happy someone finally got it to work. I really couldn't find any difference in our processes as far as the build automation went. My project has a lot more dependencies, but that didn't seem to be the cause of my problems.
Every time I published my application manually, the certificate asked for a password. This was the same password that I used to store the certificate on our build server. My coworker's publishing didn't require him to enter one. So then I thought to myself, maybe a password dialog is just sitting there waiting for input.
The reason I came to this conclusion was that I did some testing and looked at the output directory of where my files were being published. Everything was being created and copied except my ".application" file. That triggered the thought that my certificate wasn't signing the application manifest because of a certificate password window just sitting there waiting for input. The build process can't handle window pop ups.
My solution was to just create a new signing certificate with no password and this time I didn't place it in our build server's certificate store. After adding the certificate to my project I ran my ClickOnce build and it worked...FINALLY!
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