iOS Build Fails with Updated 64bit Modules

I recently updated two iOS modules to comply with the new x64 architecture requirement. They build just fine in both Xcode as well as when running the build.py script. When running lipo -info on the modules it returns armv7 i386 x86_64 arm64. I've also run the ti-64 tool on my project and it shows all modules as green. However, when I try to build my application in Titanium Studio (3.5.0.GA) with either module referenced, I get the following error:

[INFO] :   Invoking xcodebuild
[ERROR] :  2015-02-24 14:50:11.495 xcodebuild[3204:48468]  DeveloperPortal: Using pre-existing current store at URL (file:///Users/cao/Library/Developer/Xcode/DeveloperPortal%206.1.1.db).
[ERROR] :  ** BUILD FAILED **
[ERROR] :  The following build commands failed:
[ERROR] :   Ld build/MyApp.build/Debug-iphonesimulator/MyApp-universal.build/Objects-normal/x86_64/MyApp normal x86_64
[ERROR] :  (1 failure)

[INFO] :   Invoking xcodebuild
[DEBUG] :  Removing empty directories
[INFO] :   Image optimization complete
[ERROR] :  ** BUILD FAILED **
[ERROR] :  The following build commands failed:
[ERROR] :   Ld build/MyApp.build/Debug-iphoneos/MyApp-universal.build/Objects-normal/arm64/MyApp normal arm64
[ERROR] :  (1 failure)

Thanks