Images up to version 1.4 already have been hive based and the registry information was stored to *FlashDisk*\ . One common mistake is to modify the PRJ_ENABLE_FSREGHIVE varialbe in the PBXML. Please compare our default PBXML file with your one.
Probably you are already aware of that: The registry needs to be saved manually using the save registry in the update tool. There is no auto flush due to wearing issues of the Flash.
One other note: We recommend handling the registry in the way we propose it in our image. There are plenty of options how you can do it, but not all are tested very well. Specially from image 2.0 on you will be able to use the backup / restore feature of the update tool if you use the default setup.