OK, I'm not sure if this is a pak64 bug or an engine bug. :P (Also been around since r6943, where I noticed it first.)
On generating maps with high mountains/roughness this happens on the coast:
Left=pak64 r1409 (24th Feb) Right=an older version of pak96 (zoomed out to match)
(http://i.imgur.com/HS7Wu1x.png)
Notice how some tiles in the pak64 map sink beneath the water level. When generated with pak96, this doesn't happen. The image below shows the sliced underground view at the same level:
(http://i.imgur.com/QQFzxte.png)
Could be the problem, kierongreen mentioned in the other thread: double slopes that are half in water.
Ah, that'd explain the pak96 generation being fine; it hasn't got double/half images.
should be fixed in r7086