I have no doubt that the issue will be this option in CWIS > Properties > Services > Scan to mailbox > Files. As to the why, no idea. Likely if you were to run a Secure Disk Image overwrite the issue would partially be fixed.
But, having stated that, you are on the general release firmware and there have been reports of jobs occasionally getting stuck in the device with a Processing state, reboot to fix.
There have now been 8 releases since then, to fix many things, including the one it appears you are having. On the plus side, it is very easy to install, as Xerox now has a tool installer that does not require anything but a PC with a connection to the printer via LAN.
I highly suggest you go grab it here and run it to update to the latest release.