If you are first retrieving the files using get (so they are available on the build machine) when you do the checkout, you could you a Process Files step to workaround this Vault limitation.
The xml fragment below can be copied and pasted into Visual Build Pro to see an example. This hasn't been tested, but should work with minimal effort.
<step action='Process Files' type='0'>
<FileExtensions>AssemblyInfo.cs</FileExtensions>
<FilePath>c:\temp\visbuildpro\assemblyinfocheckout </FilePath>
<FilePathOnly type='11'>-1</FilePathOnly>
<FileRecurse type='11'>-1</FileRecurse>
<indent type='3'>1</indent>
<name>Iterate over folders containing AssemblyInfo.cs</name>
</step>
<step action='Set Macro' type='0'>
<MacroDescr>the above converts an absolute path to a valid Vault repository path for use by the Vault Checkout command</MacroDescr>
<MacroName>VAULT_FOLDER_PATH</MacroName>
<MacroValue>[Replace(Replace("%PROCFILES_FULLPATH%", "c:\temp", "$"), "\", "/")]</MacroValue>
<indent type='3'>2</indent>
<name>Populate Macro with Vault compatible path</name>
</step>
<step action='Vault' type='0'>
<Command>checkout</Command>
<Host>%VAULT_SERVER%</Host>
<Project>%VAULT_FOLDER_PATH%AssemblyInfo.cs</Project>
<Repository>%VAULT_REPOS%</Repository>
<ShowCmd type='11'>-1</ShowCmd>
<Username>%VAULT_USER%</Username>
<indent type='3'>2</indent>
<name>Checkout the AssemblyInfo.cs file</name>
</step>
Hope that helps...