Setting TeamCity agent.work.dir from Custom Build - build

I'm setting the teamcity.build.checkoutDir configuration parameter via the 'Run Custom Build' dialog as I want to control the build location.
When looking at the 'Build Parameters' page of the build, I can see the teamcity.build.checkoutDir parameter is correctly using my set value, but the 'Actual Parameters on Agent' value always remains set to the default checkout path.
I've tried setting the Version Control Settings->Checkout Directory to Custom Path and the teamcity.build.checkoutDir parameter still does not use my custom setting.
Please can someone help me with this?
Many Thanks!

You can't change the value of teamcity.build.checkoutDir. All the teamcity.build.* variables are read-only.
You can change the checkout directory by editing the VCS root settings.
Edit the build configuration
Select Version Control Settings
Next to Checkout Directory choose 'Custom Path' from the drop-down.
You can also set a custom path by using custom client mappings for the VCS.

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I am creating an msi using VS installer but I've run into a problem. What I need to do is take input from the user, a server name/port and username/passsword. Once I have this I need to verify that they are correct then continue with the installation r return to the input page.
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