Update: Downloading the latest version of hte Sidekick tool fixes the problem mentioned here. See this comment from Matan:
"Please download the latest version of the MSBuild Sidekick - that should take care of the non-MSBuild parts not being saved problem.
We've released a patch for it less than a day after the release.
Regarding the absence of Team Build elements from the UI, please note my post about schema-support. This is a known issue and we are working hard to solve it as soon as possible.
When I first found out about MSBuild SideKick, I was excited. I thought that finally there's a slim chance that I won't have to edit dreaded XML files, and instead use a point and click interface, like god intended. I even pointed to Matan's Blog, which is one of the guys behind this tool so you can send comments his way.
I then tried to edit a TFSBuild.Proj file using MSBuild Sidekick. It seemed to work well except for one major problem:
Sidekick only uses the MSBuild Schema for the various properties inside it, so it leaves out essential properties that Team Build needs like the Build Machine Name. So, when you save the file through Sidekick, and then check it in and try to run the build through the Team Explorer Addin, you get a nice error message that states that the Build Machine Name is missing from the build type file.
So much for helpful. Can someone please pick up the glove on this? It's already dirty, tainted and muddy, and it will be trampled by people jumping up and down with ange if someone doesn't pick that glove up pretty soon (that someone just might be me!)