WiX v3.0 and v3.5 executables are available in .zip form and x86 and x64 .msi packages. The x64 .msi package was originally created because we need to install the WiX targets and tasks for 64-bit MSBuild into a 64-bit directory, something that’s not supported for x86 packages. Late in the WiX v3.0 development cycle, Jason made a change that lets 64-bit MSBuild use the targets and tasks in the 32-bit directory tree. Unfortunately, the special property used to allow that is present only in MSBuild v3.5, not MSBuild v2.0, so we still create the x64 .msi package.
Creating the x64 .msi package isn’t a huge burden on us but it’s led to some confusion, so we’d like to get rid of it. If you use 64-bit MSBuild 2.0 and the x64 WiX .msi package, please respond in the comments. If you use MSBuild 3.5 or the .zip WiX package or by checking WiX in to your source-control system, you’re not affected and can use the x86 WiX .msi package.