I have encountered a problem that I can't resolve. When I print to PDF from Autocad and than print this PDF, everything looks fine. But when I import it in Indesign (or Illustrator) and print it from there or to PDF, some thiner or dotted lines disappear - are not printed correctly. I don't manipulate PDF once it's imported so ... what's going on?
There appears to be often problems from AutoCAD pdf's for this sort of work. I would try this, as a work-around. Export as an EPS from AutoCAD and place that in InDesign. Does it work any better?
As a side option, we make (I represent Markzware, the software developer) a PDF to InDeisgn conversion filter called PDF2DTP. That however, will likely cause more work then you need, for you are not manipulating the PDFs once imported.
I think the export as EPS and place that will solve your issues - hopefully anyway!
Auto CAD files have often a problem with the width definition. This does not allow X-standard files for printing. Maybe that in Acrobat a line correction before importing to InDesign will help. In Acrobat Pro go to Tools > Print Production > Correct Hairlines.
(Maybe the actual texting in Acrobat is a little different because I translated it from German back to English)