Solution
In newer versions of Acronis OEM (such as the ones that come pre-loaded on our PXIe devices) the restore functionality clears the recovery partition where the factory restore lies. This means that the factory re-image will only work once using the Acronis software on PXIe controllers.
After recovering once, you have to use the Acronis application in Windows to create a recovery media (typically USB) for future recoveries. There is no way to get back to the true factory state with an extra Acronis partition from NI.