I was using devenv to build the project through CruiseControl.Net. I switched to the MSBuild task and specify my OutputPath in the buildArgs and it works as I expect. This wasn't the solution I was looking for but it will do.
<msbuild>
<executable>$(v4_MSBuild)</executable>
<workingDirectory>$(SourceRoot)$(TrunkDir)project1</workingDirectory>
<projectFile>$(SourceRoot)$(TrunkDir)project1\main.sln</projectFile>
<buildArgs>/p:Configuration=Debug;OutputPath="bin\Debug" /v:n</buildArgs>
<targets>Build</targets>
<timeout>900</timeout>
<logger>C:\Program Files (x86)\CruiseControl.NET\server\ThoughtWorks.CruiseControl.MsBuild.dll</logger>
</msbuild>