Something like this already happened multiple times to our customers.
After analyzing the corresponding GRP files I've noticed that these e-mail were completly missing their headers in the GRP file (no headers at all, they were starting directly with the "body").
We opened a ticket about it but no real solution was given to us.
No idea why the headers are gone and they lost forever (unless you have a backup dated from before the headers disappeared).
For some of them we have old enough backup to be able to restore them for the customer and also it showed that the mail was correct when received in the first place so SM corrupted them at some point ...
When working on this issue I wrote a tool in python that scans GRP files and check every mail if they contains at least the mandatory headers, and we unfortunately found out that many customers were affected with this (hopefully on kinda older mails).
I would say that at some point some builds of smartermail was causing this and it was resolved later on.
Now it seems you're talking about kinda recent e-mails so I guess I should run a new global scan sometimes soon ....
Hopefully my testing domain seems clean...