This has happened twice today, I got killed by a nuker, and my HUD says my bounty is still 385 or w/e, and it wont change.

My "all players" list shows me at 40, but the HUD says 385....

Does this only occur when you are killed by nukes? What about other weaps?

yes, only nukes, and for some reason, it seems to only be when someone "exploits" IE, launch, then dock. I'll test it further.

Interesting. I wonder if the nuker gets any bounty or points for the "kill"

nope, happens at random