Most of the time it comes down to the fact that some bvh files are better than others -- especially the free ones, many of which were captured in the early aughties using 1990s and aughties technology.
Sometimes how well a bvh maps and re-targets to an armature depends upon the proportions of the original motion capture actors versus the proportions of the armature.
I've not had one displace the eyes like the OP desbcribed -- that could be another issue, like parenting -- but the drop through the floor thing usually has to do with where the bvh file thinks the floor is.
Most of these can be corrected with the editing facilities in MakeWalk, though some require more effort than others.
The best -- and perhaps only -- documentation for how to do this is here:
https://thomasmakehuman.wordpress.com/m ... dit-panel/
Following this tutorial helps with applying the basics:
https://thomasmakehuman.wordpress.com/m ... ning-feet/