I've really heard about this issue alot this past year. Seems that Linden Labs, when they converted over to the Havok 4 physics engine wound up breaking their own script function that returns a prims bounding box if the prim has a dimension less less than .05 in size. This causes Prim.Docker to misalign these small prims. I'm hoping that they can fix this because it is really annoying.
See the bug report submitted for this issue here:
http://jira.secondlife.com/browse/SVC-2741
