I can certainly conclude that it is NOT due to mods, but mods may make the bug more likely.
Source: As I mentioned in the OP, this was happening to my friends and I on my vanilla server.
Quick look of the server logs shows
[11-11-18 10:00:16] 76561197967692106 "Jaximus" fully connected (13514,10718,0).
[11-11-18 10:00:18] user Jaximus died at (13514,10718,0) (non pvp).