I recently had difficulty building a deployment project that
packaged a set of 64-bit DLLs. The error was "File <a DLL in my
solution> targeting 'AMD64' is not compatible with the project's
target platform 'x86'".
This confused me because all my projects were targeting x64. It
turns out that the project's target platform referred to here is
the target platform of the deployment project itself,
apparently set to x86 by default.
Clearly the deployment project needs to be targeted at 64
bit. Ordinarily you can just right-click on a project and
select "Properties" to open a dialog that contains a "Platform
Target" setting, but you will NOT find this setting for a
deployment project.
The answer is to select the deployment project in the solution
tree, then open its Properties tab. You will then see
a "TargetPlatform" option and you can select "x64":

For an excellent overview of target platforms see
http://visualstudiohacks.com/articles/visual-studio-net-platform-target-explained/