You inspired me. PrimoCache does caches MFT. However, during the initial stage of Windows booting, there is some read and write access to the Windows partition before Windows loads the PrimoCache driver. So MFT might be updated before PrimoCache is loaded, but flushed after PrimoCache is loaded. Due to "no refresh on shutdown", the updated MFT may not be finally written to disk, causing the actual file content to be out of sync with the MFT.
Another possibility is that, as SnowReborn mentioned, some special applications can bypass the logical volume and directly read and write hard disk sectors. This can also cause desynchronization, damaging the system.