Hi,
the two paths that you see on the Path page are the paths for the 'AVR-GCC' and 'GNU Make' as set on the Preferences -> AVR -> Paths page.
These two paths get prepended to the the paths that CDT already knows ( Preferences -> C/C++ -> Build Variables -> Path ), which in turn should be the PATH from the shell that Eclipse was started in.
Could you please check if /bin is in this path?...
I have started to work on this Bug and the obvious culprit is not the AVR Plugin but the WindowRegistry Class from CDT.
There is already a bug report that this class is not working on 64bit Windows. https://bugs.eclipse.org/bugs/show_bug.cgi?id=236330
To fix the Problem I will need to check the return value of WindowsRegistry.getRegistry() and if it is Null then either fail gracefully or...
