[ZBrush] Overlapping geometry on imported assets

Hello,

I've been having a problem for a while now that I've mostly just ignored or worked around, but I figure it's time to save time by finding an actual solution. My workflow for creating high-poly assets is to create boolean primitives in Maya, then import them to ZBrush so I can use its Live Boolean function. Once it's all finished, I Dynamesh and smooth crisp edges to my liking. This has been working great for me, with one nagging problem.

Occasionally whenever I import geometry into ZBrush from Maya, the geometry is duplicated directly over itself in a perfect 1:1 ratio. Obviously it's very hard to spot because of this. The problem occurs when I try to apply my booleans into one mesh. The geometry tries to overlay its own overlapping topology and freaks out, creating a buggy monster that doesn't like being Dynameshed.

Here are some photos:

This is a simple mesh that I completed using a few booleans and it's ready to apply into one mesh. The topology looks completely fine in this state, if I were to preview it.

But when I apply my booleans, you can see that one of the primitives has overlapping geometry and gives you this monster instead of a decent cylinder. You can see the difference between the green, blue, and pink booleans that do not have overlapping geometry.

If I import the primitive into Maya, I can double-click to select all faces and delete, giving me only one mesh.

This seems to only occur when I import meshes over existing meshes in ZBrush. Since importing always overrides the selected subtool, I normally import assets by inserting a Sphere3D, then importing my primitives from Maya over the Sphere3D. How can I fix this issue? Is this a known bug?

Thanks for the help.

I'm getting pretty tired of all the importing and exporting...