I think the causes may be even more varied, but seems to be happening when calculating warp jumps and during the actual jump itself.
Tried our server now on 2 completely different hardware set ups and the results are identical; server runs for about an hour or so, then we get regular 'hangs' of about 5-10 seconds.
I'll post the logs from work tomorrow.
Still, this hasn't stopped me playing this game and putting in 68 hours in the last 8 days :P
(Loving your work!)