It looks like Visio 2013 does some sort of (incorrect?) anti-aliasing in this case.
Some user example form
another forum below.
1. Overlapping lines in the exported file (you can see the position where the lines overlap - what the heck?!). In Visio 2010 and below, these artifacts (if they exist at all) are much less apparent.
A
Visio file, containing two overlapping lines 3/4pt, exported to EMF with Visio 2010 and 2013:
Visio 2010:
Visio 2013:
2. There appears to be also a problem with embedded objects, like embedded objects (e.g. Word or Excel). It appears to be fixed with some update for PDF in Visio 2013, but it looks the problem is still there for the metafiles..
Visio file (with embedded Word object text):
EMF (exported by Visio 2013):
EMF (exported by Visio 2010):
This makes me a sad panda :(
Maybe there is some setting to fix that?