Hi everyone,
I just wanted to chime in, I have been having these same problems with SB and my inkscape created DXF files since the end of July. I had no problems with them prior to that time. I know SB updated their software on or around July 30.
I contacted SB though their online chat help service and they told me to delete the apex file as well. It did not work. I have tried saving my dxf files several different ways in inkscape but the result is always the same when I upload to SB. Lots of overlapping lines and nodes that would cause a huge mess cutting vinyl.
I have been searching for an answer and can't find one, my conclusion is that the problem lays with the July update to SB. It frustrates me, I enjoy creating my own art and feel like Silhouette wants me to purchase only their files or upgrade to the more expensive design space software.

I will keep following this thread. If I find a solution I will post it here.
I hope there will be more information in the future about this subject and a possible fix, maybe even from SB.
Have a great day guys!