It's difficult to say why it's happening. A common issue is that some slave node cannot find the plugin files (as the shader for Mental Ray or the dll's for VRay), but in this case the failing nodes never render the trees. So, by your problem description the plugin seems to be installed correctly.
What renderer are you using ? Do you use proxies, and where are them stored ?
If you can, please post a failed framed, to see if we can get some useful info.