From the Log it is usually hard to say what went wrong in the past. One thing we recommend and also was in the old production programming process was to do a “wipe” of the flash disk while doing production programming. The reason is, that there have been some issues with the flash driver in images before 1.3 which could have lead do such behavior. In case you did not do a wipe or NVFlash / Recovery Mode for production programming, it could happen, the issue is still kept in the Flash and can also show up in image 1.4 and later.
Also your issue really looks like the bug I mentioned above, it is always a good choice to go for the 1.4 image. To make use of the improved flash file system handling, you have to either use NVFlash to upgrade to 1.4 or use the new Update Tool 6.0.5 or later and upgrade your system using the “cfg” file, not the *.nb0 files. Copy these files in to the unziped Image files folder and choose the WinCE version you want to flash in the new Update Tool. This will update everything including Image, Bootloader and flashfilesystem handling.