Here is a small unexpected aspect of the NetLogo-Mathematica Link. There's 
also an easy workaround, but it's surprising that when starting the link 
with …

<<NetLogo`
NLStart["/Applications/NetLogo 6.0.4"]

and (eventually) finishing with

NLQuit[]

but keeping the current Mathematica kernel running, and starting up the 
link again with an intended different version of NetLogo, like this

<<NetLogo`
NLStart["/Applications/NetLogo 6.0.1"]

the actual NetLogo version usage doesn't change. The 6.0.4 version still 
boots. The workaround is to quit the Mathematica kernel before using 
<<NetLogo` again.

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