It is possible that the db commits have failed and hence few data is missed. Could you trace the scenario at the time you are seeing the issue? Comparing it with the working scenario would help us in coming to the root cause.
I feel like that for the case for which the properties are not getting populated is not having a proper class hierarchy upto Work- because of which the properties are not getting mapped on to the table level and hence not reflecting on the case level. Please check fr the Data base Class Mappings tool for verifying whether the properties are mapped properly or not.
Also, as you said that this is happening after server restarts, I feel that this might be happening due to some hotfix installation. So, I would request you to go by any hot-fixes you might have installed recently.