Missing NIB's on Build

What would cause NIB to be missing from the app package on one build then be there the next?
This includes random xib files including sometimes the MainWindow. Happens in the Simulator and multiple devices.
This project has gone through quite a few updates to XCode and a migration from CVS to GIT.
I tried removing all the references and reading the files to the project (a long and arduous process).
I have checked and rechecked and triple checked the Build Phases >> Copy Bundle Resources.
It seems like some nibs are just getting left out in the build process?
Any thoughts on this issue beyond what I could glean from Google and searching these forums?
Randall S. Fish <><
Uncaught exception: Could not load NIB in bundle: 'NSBundle </Users/rfish/Library/Application Support/iPhone Simulator/5.0/Applications/4F02A642-03BD-4BB8-A1F4-BF6938C1E461/MyApplication.a pp> (loaded)' with name 'MainWindow'
2013-07-30 11:23:02.586 MyApplication[20758:c07] Stack trace: (
    0   CoreFoundation                      0x0291406e __exceptionPreprocess + 206
    1   libobjc.A.dylib                     0x020ccd0a objc_exception_throw + 44
    2   CoreFoundation                      0x028bca78 +[NSException raise:format:arguments:] + 136
    3   CoreFoundation                      0x028bc9e9 +[NSException raise:format:] + 57
    4   UIKit                               0x015a9838 -[UINib instantiateWithOwner:options:] + 2148
    5   UIKit                               0x015ab010 -[NSBundle(UINSBundleAdditions) loadNibNamed:owner:options:] + 157
    6   UIKit                               0x0138b14a -[UIApplication _loadMainNibFileNamed:bundle:] + 58
    7   UIKit                               0x0138b461 -[UIApplication _loadMainInterfaceFile] + 225
    8   UIKit                               0x0138a7c0 -[UIApplication _runWithURL:payload:launchOrientation:statusBarStyle:statusBarHidden:] + 278
    9   UIKit                               0x01399743 -[UIApplication handleEvent:withNewEvent:] + 1027
    10 UIKit                               0x0139a1f8 -[UIApplication sendEvent:] + 68
    11 UIKit                               0x0138daa9 _UIApplicationHandleEvent + 8196
    12 GraphicsServices                    0x02aa7fa9 PurpleEventCallback + 1274
    13 CoreFoundation                      0x028e81c5 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE1_PERFORM_FUNCTION__ + 53
    14 CoreFoundation                      0x0284d022 __CFRunLoopDoSource1 + 146
    15 CoreFoundation                      0x0284b90a __CFRunLoopRun + 2218
    16 CoreFoundation                      0x0284adb4 CFRunLoopRunSpecific + 212
    17 CoreFoundation                      0x0284accb CFRunLoopRunInMode + 123
    18 UIKit                               0x0138a2a7 -[UIApplication _run] + 576
    19 UIKit                               0x0138ba9b UIApplicationMain + 1175
    20 MyApplication                 0x001a23d2 main + 290
    21 MyApplication                 0x00002905 start + 53
    22 ???                                 0x00000001 0x0 + 1

We usually copy the xib files to a temporary location with the .m and .h files then go through and rename the files and open them and change the class names, then add the files into the project as new files.
We have never done this with the MainWindow that file has been consistant throughout the lifecycle of the project.
It is hard to be 100% sure on the Case of the file names because there are so many. However, I can compile then browse to the .app file browse package and see that the MainWindow.nib file is missing. Re-run the build and repeat the steps and the MainWindow.nib is there.

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You’re using the default TFS 2010 build process template in your build definition to build solution?
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