it's a common problem and many are searching for the right answers.
I have exactly the same, and sometimes find a solution for a single object but i am not able to find the real solution.
Most of the time it occurs when two tranparencies overlap each other and both transparencies have the same render order.
For instance a tree with a waveset on the background is a problem, turning around the same tree it disappears when it has another background.
The alcscript to force late rendering helps for this, but not always.
tree:
visual:
renderlevel:
major:
- late
minor:
- blend
The transparency pixels around the tree edges can course the problem.
I had it introduced when i altered the size of a texture from 512 to 256.
Lontahv found a solution for this and made a wiki entry for this a few days ago.
It realy helps in many cases i advise to give it a try and filter your texture with this tool.
http://www.guildofwriters.com/wiki/Alpha_Textures_Removing_EdgeYou can see the difference in my thread of turtle isle, before and after filtering.
http://forum.guildofwriters.com/viewtopic.php?f=7&t=3809&start=30