Ok, So I am running a load of plugins :

1. Zonemanager has 0 zones,
2. TruePVE is running

Player Logs out, and after a few minutes he dies to Suicide.
I can't figure out what is killing him. It happens to two players who stay together.
If I go to sleep in the player's base, I die. If I go to sleep elsewhere I don't?

You could have a phantom Zone open, I would unload Zone Manager and see if it still happens.

I've seen this before, in my case it was sleeping in a "monument" that was killing the player, the "monument" was the train tunnel that had generated much closer to the surface than usual (or the terrain was unusually low). Check whats under the base.

what is the distance to the closest monument ?

about a half a grid away, so it could be that...