Yes, I hate this standard behavior, but TFS will output everything to the same folder by default, and then you will get various errors depending on which order msbuild compiles your projects if you have references with the same name or even project outputs with the same name.
The easiest workaround is to use the AsConfigured
option on the Process tab, '2. Build' -> 'Output location' of the build definition window. This keeps your normal source structure intact, but I think you will lose support for automatically dropped outputs (i.e. you will have to provide a script to do that yourself). If you are only using TFS Build for validation, this is the cleanest approach.
You can also use the PerProject
setting and split up your projects into two distinct solutions, perhaps suffixed by platform (we've done that numerous times in our company). Then, you specify both solutions to the build process and it will create two separate folders in the output, one for each solution.
This is all assuming you are using TFS 2013. In TFS2012, there is a similar option but it is in '3. Advanced' -> 'Solution Specific Build Outputs'. You will probably have to go this route if you are using TFS2012 or you will need to modify the default workflow yourself to add your own logic.
EDIT:
From your comment to the other poster I see you are using TFS 2010. Well... I think this was absolutely not supported at that time, I remember having similar problems, but we upgraded to TFS 2012 and all was well.
I think your only option is to either create two separate build definitions and build each solution that way, or you will need to checkout the xaml workflow and edit it with your own logic. Perhaps downloading the TFS2012 template and "porting" it to TFS2010 would be a better approach since at least you would not be reinventing the wheel that way.