As reported in (https://bugs.launchpad.net/ubuntu/+source/blender/+bug/1575695):
HOW TO REPRODUCE:
1. Start Blender.
2. Maximize its window.
3. Click on the menu "File -> Save Startup File".
4. Close Blender, and start it again.
RESULT:
The window is not maximized.
ProblemType: Bug
DistroRelease: Ubuntu 16.04
Package: blender 2.76.b+dfsg0-3build1
ProcVersionSignature: Ubuntu 4.4.0-21.37-generic 4.4.6
Uname: Linux 4.4.0-21-generic x86_64
ApportVersion: 2.20.1-0ubuntu2
Architecture: amd64
CurrentDesktop: Unity
Date: Wed Apr 27 16:04:02 2016
InstallationDate: Installed on 2016-04-26 (0 days ago)
InstallationMedia: Ubuntu 16.04 LTS "Xenial Xerus" - Release amd64 (20160420.1)
SourcePackage: blender
UpgradeStatus: No upgrade log present (probably fresh install)