different checkout behaviour on server checkout and agent checkout

I have a TC build (build 46812) that uses 2 Plastic SCM VCS roots.  I need to use both of these roots within the build.  I have set up the checkout rules as below;

+:.=>project1 for project 1's VCS root

+:.=>project2 for project 2's VCS root

When the checkout mode is set to 'Always checkout files on server' the 2 projects appear in the working directory as;

\project1\<20 or so project folders and files>

\project2\<30 or so project folders and files>

This is my happy place as it is exactly as I want.  The only problem is it takes a long time to run.  I have always found the checking out onto the agents is significantly quicker - the problem I have found is that when the checkout mode is configured to 'Prefer to checkout files on agent (recommended)' or 'Always checkout files on agent' the code from project 2 does not get put into a separate folder but is copied directly to the root folder overwriting the code from project 1 and I end up with this

\<30 or so project folders and files>

is there a way to achieve my happy place without using the 'Always checkout files on server' checkout mode?

many thanks in advance (I also hope this explanation makes sense)