We've found that this is related to the Windows "File System Tunneling" capability.
The capability is described here: Windows NT Contains File System Tunneling Capabilities
There are several options to resolve this issue:
1. Turn this feature off on the servers running Wowza Media Server
The above support article also includes the registry setting to add or change in order to turn the "file system tunneling" capability off. It will require a reboot for the registry setting to take affect. With this feature turned off the file creation times should be correct.
2. Track the file modification time instead of tracking the file creation time, which is a more accurate representation of the recording time.
3. Create a custom module that uses IMediaWriterActionNotify to rename the file to a unique filename that includes the file recording time as part of the filename.
More information can be found here: How to use IMediaWriterActionNotify to programmatically move and rename recordings of live streams
Incorrect file creation date in Windows XP/Vista