I've just migrated our Team Projects from TFS2008 to a new TFS2010 server and everything seems to be going well except for one thing (so far).
I have a TFS build that worked fine on TFS2008 and works fine on my machine, but when it is built by TFS2010, the build order for the solution is not followed. It's just one solution that's being built, but it has a dozen or so projects in it. All dependencies are set up as project references.
I've found this question/answer Build order and dependencies not preserved on upgrade from VS 2008 to 2010 with msbuild, but it's a slightly different scenario. We haven't upgraded the solution to be used in VS2010, it is still a VS2008 solution.
I'll keep looking for an answer. Checking here in the hope that someone has seen this before and solved it.
I've also found this post that points to another page referenced from the first link. It looks like the two problems have a similar cause and my two best options are to upgrade the solution to VS2010 or manually edit the dependencies into the solution file.
I'll probably be upgrading the solution soon anyway, so maybe I can move that ahead of schedule.
I'll leave the question open for other possible solutions.