I've been testing out giant caves on my server running an older version of minecraft 1.5.1 (using plugin version R: 1.5.1-R0.1 R2 ) and started using the plugin a couple of days ago. Everything is working and I've been using a combination of dynmap and digging around to find them. Very Very easy to use.

The biggest problem I'm finding is when merging mine shaft tunnels into the caves weird things occur. Many times platforms made from wooden planks (which I assume is a natural generation for the mine shafts when crossing chasms and other natural occurring big rooms). But because of the size of the big caves they just randomly float as depicted in the picture below.

This needs to be fixed as it breaks the environment of the game and looks akward for players.

Don't remove mineshafts completely from these rooms, such as showing them running along the floors, sides and ceiling (which would be cool). Just remove the floating structres within the spaces would be nice.

I haven't seen this happen to dungeons or strongholds but I assume the same thing is happening with them as well and Should be kept in mind. As I said before I'm really enjoying the exploration elements of the mod. But this bug is immersion breaking and needs to be changed.

Cheers

This has been asked before: It is impossible to do without having a database of changed blocks running in the background.
The reason why is that villages, mineshafts and strongholds are generated last in the Chunk Population stack. I don't know how to change that without instantly breaking craftbukkit, so it will have to stay, sorry.