This is reported too often to be a simple file permissions issue. It is probably a concurrency problem with opening, reading, and writing the config file. It started happening after we merged #247 and then fixed some other concurrency issues (r35718, r35721, r35726, r35727, r35744, specifically 97b5aa2).

Example reports:

• http://seclists.org/nmap-dev/2016/q2/70 (saving in Program Files on Windows)
• http://seclists.org/nmap-dev/2016/q2/244 (saving in %userprofile% on Windows)
• http://seclists.org/nmap-dev/2016/q2/197 (saving in $HOME on OS X)