Might be a red herring (as I don't know *how* DeployAnywhere injects these things), but assuming it's all sysprep in the end.... then it might be an issue with hardware detection being disabled.
You see sometimes people in environments with just one standard piece of hardware make their mini-setups faster by tweaking the sysprep xml. They override the default value of PersistAllDeviceInstalls in the XML used to sysprep the machine to stop sysprep cleaning out the PnP drivers.
You can judge if this is happening by looking closely at the machine in mini-setup and checking for the device detection phase.
Take a look at this,
https://technet.microsoft.com/en-us/library/cc722095(v=ws.10).aspx
So, in the orginal syspreping you either want this key to be missing entirely, or set explicitly to false in the Microsoft-Windows-PnpSysprep component.
<PersistAllDeviceInstalls>false</PersistAllDeviceInstalls></component>
If it was set to true, then PnP devices weren't uninstalled at sysprep time, and won't be re-installed during the specialize pass.