I can see in your graph you are translating between coordinate systems- you are on the right track here
It is most likely something to do with internal coordinates vs project base point etc.
I have taken a slightly different approach in the past by processing the XML clash report from Navisworks using Dynamo
(rather than using the Dynaworks nodes- I found the performance of Dynaworks was very slow)
Refer Dynamo: performance
My suggestion is to troubleshoot using a file with just one or two clashes- and compare the object intended position vs actual & work out where it is going wrong. Since you are feeding in the name to the comments parameter- you should be able to correlate the two