Symptom

Following an upgrade to the latest version of XCode (3.7+), proxies are being created successfully, however, playback of the output files are showing as green/transparent in certain media players (for example, Quicktime/Premiere Pro).

Resolution

The underlying issue here stems from how Windows servers cope with running video codecs, more specifically changes to video codecs. In the earlier versions of XCode (Below 3.7) Main Concept codecs V9 were used, these can be seen in the Codecs folder of your XCode installation. When XCode first attempts to use these files, Windows creates a registry entry (This is user specific). For reference:

HKCU\Software\MainConcept
HKCU\Software\MainConcept (Broadcast)

If you cannot log into the XCode server as the Windows User set to run the XCode service, you will need to change the registry differently:

HKEY_USERS\[USER GUID]\Software\MainConcept
HKCU\[USER GUID]\Software\MainConcept (Broadcast)

The problem starts to arise when XCode is upgraded from an older version to the new, due to certain codecs being upgraded from V9 to V10 (IPV will RARELY change codecs, however in this instance it was necessary). As the registry does not reference the version number, when XCode is run following the upgrade the registry only gets partly updated, causing some proxies to play back slightly incorrectly in some media players. 

To resolve the issue, it is necessary to delete (or rename) the MainConcept directories so that XCode can remake these upon its next run. 

NOTE: Please back up these registry entries for rollback if deemed necessary.