[all variants] Files disappearing after rebooting into Windows

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http://ubuntuforums.org – I've noticed lately that some files are disappearing when rebooting into Windows from Linux. I have a partition formatted as exFAT that I use to store files that I need in both Linux and Windows. I can create a file in Linux, reboot into Windows, check the partition, and it's gone. Is it possible that Linux isn't flushing the cache to disk for whatever reason when shutting down? Or is there a different problem? For the record, when shutting down, I issue a "sudo shutdown -hP now". (Hardware)