A recent question on Ask Wireshark (
http://ask.wireshark.org/questions/30890/makensis-makensis-path)
On all the 64 bit systems I have, the env var PROGRAMW6432 is set to "%SystemDrive%\Program Files", so it appears to me that the change, despite the added comment to config.nmake, doesn't look for makensis.exe in "%SystemDrive%\Program Files (x86)" at all.
The nsis installer will default to "%SystemDir%\Program Files (x86)", so I think the second check should use the env var ProgramFiles(x86), which again on all my 64 bit systems points to the default nsis install location.
Thoughts anyone?