Circular plane disappears when solidifying mesh

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I've made an STL file in blender. When I import it to meshmixer and size it up, everything is fine, but when I try to solidify it, the circular face at the bottom disappears. I've tried the different solid types, I've maxed out Accuracy and Density, and minimized Culling Threshold. I've practically tried every option in the solidify interface. Any advice?
Mind you, in Blender there are plenty of non-manifold edges, intersecting faces, zero faces, etc. There's just too many and I don't know how to fix them all. If that's the problem, any tips on how I should address that would be appreciated. I've already gone through and closed up anything that was actually unintended, but otherwise everything seems to be in good order, blender just keeps telling me it's not. I've installed 3d print tools in blender, but when I click "make manifold" it closes up ports I need for a switch and a charging board. I should note that there are rails that intersect with the bottom face, which I mean to meld into the bottom face when it prints.