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It is certainly an OS X issue. Assuming the default shell is configured, when Terminal starts up it runs the script file ~/.bash_profile, which usually modifies the PATH environment variable. You can do the same thing in Mathematica with SetEnvironment["PATH" -> Import["!source ~/.bash_profile; echo $PATH", "Text"]] After which Environment["PATH"] ... 7 I think this is an OS X issue. Note that if you launch Mathematica from a terminal, you will get the value of Environment["PATH"] which you expected. For GUI applications that are started through Finder/LaunchServices, the environment (and$PATH in particular) is different and determined by the OS (this is a related recent question that had to do with ...
Let's override the Run so it stops acting up. Needs["NETLink"]; InstallNET[]; Unprotect[Run]; Run[x___] := Module[{t, p}, LoadNETType["System.IO.Directory"]; DirectorySetCurrentDirectory[Directory[]]; t = NETNew["System.Diagnostics.Process"]; t@StartInfo@FileName = "C:\\Windows\\System32\\cmd.exe"; t@StartInfo@Arguments = "/c " <> ...