The reason for that is that the cRIO-9012 is running VxWorks as the underlying RTOS. For the LabVIEW RT user the differences between using a VxWorks and an ETS RT target are pretty minimal but there are a few difference. In order to keep the experience on VxWorks targets the same; Windows/ETS style paths are used in LabVIEW RT and under the hood they are converted to Unix paths. However, as you found the 'Path to String' and 'String to Path' primitives do not convert from Unix to Windows paths. Other difference can be found in KB 44HDTKQ0: "Frequently Asked Questions (FAQ) for NI cRIO-9012".
I was actually more surprised to see the Current VI's Path function return a Windows style path. I guess it's just something I never looked at before for some reason. But them it seemed if it returns a Windows path, it should stay a Windows path.