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Did you download the new MDT installer compatible for Inventor 2012 at http://usa.autodesk.com/adsk/servlet/pc/item?id=13
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Well, I downloaded the new MDT2009 files per the link above but could not, for the life of me, get around the infamous....
"Failed Installation aborted, Result=1603"
Gave up with those files, installed Inventor 2010, then installed MDT2009 from my 2 year old zip files, then uninstalled Inventor 2010 and all is well.
(I wonder what the difference between these sets of MDT2009 installation packages are)