The two obvious questions: are you encoding the message somehow when you save it to the database and are you decoding the message somehow when retrieving it again? Can you keep round-tripping it without corruption?

Then consider sending two identical messages to yourself via the different methods and comparing them, headers included. If they differ in any way other than in timestamps and message IDs then you can analyse that and dig deeper into what's going on.

Don't forget the value of an SSCCE. Strip out everything you don't need and see if and when the problem is resolved. If it isn't, you can post the resulting SSCCE here for someone to look at.