Interacting builds and cleaning sources on build agent

It looks like I have an issue with builds that may be interacting with what sources they're getting.  I have a situation where each build has 45 checkout rules, the first of which is the branched source and the other 44 are shared third party libraries within our source.  I'm using server-side checkout.

After I got this set up, someone checked into TFS one changeset with sources from multiple branches.  Then different builds broke for no reason.  When I cleaned sources on the builds, however, they passed.

So it looks like I may have to clean sources before the builds to get this to work.  What I'd like to do is make the agent's sources get cleaned and the server just hands the sources it has cached to the agent.  Is this possible to do?  If not, why not?

Does the abovementioned scenario strike you as something that wouldn't work in TC 4.0.2?

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