java ignores menu and font size Unity preferences

When running a Java application (Stanford Protege Desktop 5.0.0 - http://protege.stanford.edu/) the user interface displays menus within the main application frame. However, the Settings, Appearance, Behavior, "Show the menus for a windows setting" is set to "In the menu bar." In addition, the font size shown in the Java application is much smaller than that shown in other applications. The Settings, Universal Access, Seeing, "Large Text" setting is On.

ProblemType: Bug
DistroRelease: Ubuntu 16.04
Package: unity 7.4.0+16.04.20160526.1-0ubuntu1
ProcVersionSignature: Ubuntu 4.4.0-24.43-generic 4.4.10
Uname: Linux 4.4.0-24-generic x86_64
.tmp.unity_support_test.0:

ApportVersion: 2.20.1-0ubuntu2.1
Architecture: amd64
CompizPlugins: No value set for `/apps/compiz-1/general/screen0/options/active_plugins'
CompositorRunning: compiz
CompositorUnredirectDriverBlacklist: '(nouveau|Intel).*Mesa 8.0'
CompositorUnredirectFSW: true
CurrentDesktop: Unity
Date: Sun Jun 26 17:51:59 2016
DistUpgraded: Fresh install
DistroCodename: xenial
DistroVariant: ubuntu
EcryptfsInUse: Yes
GraphicsCard:
 Intel Corporation Sky Lake Integrated Graphics [8086:1916] (rev 07) (prog-if 00 [VGA controller])
   Subsystem: CLEVO/KAPOK Computer Skylake Integrated Graphics [1558:2425]
Lsusb:
 Bus 002 Device 001: ID 1d6b:0003 Linux Foundation 3.0 root hub
 Bus 001 Device 003: ID 04f2:b550 Chicony Electronics Co., Ltd
 Bus 001 Device 002: ID 8087:0a2a Intel Corp.
 Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
MachineType: System76, Inc. Lemur
ProcEnviron:
 LANGUAGE=en_US
 PATH=(custom, no user)
 XDG_RUNTIME_DIR=<set>
 LANG=en_US.UTF-8
 SHELL=/bin/bash
ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-4.4.0-24-generic.efi.signed root=UUID=7aecd352-8a3f-4ce9-88b8-0fc048dc9660 ro quiet splash vt.handoff=7
SourcePackage: unity
UpgradeStatus: No upgrade log present (probably fresh install)
dmi.bios.date: 11/29/2015
dmi.bios.vendor: American Megatrends Inc.
dmi.bios.version: 1.05.06RS76
dmi.board.asset.tag: Tag 12345
dmi.board.name: Lemur
dmi.board.vendor: System76, Inc.
dmi.board.version: lemu6
dmi.chassis.asset.tag: No Asset Tag
dmi.chassis.type: 10
dmi.chassis.vendor: System76, Inc.
dmi.chassis.version: N/A
dmi.modalias: dmi:bvnAmericanMegatrendsInc.:bvr1.05.06RS76:bd11/29/2015:svnSystem76,Inc.:pnLemur:pvrlemu6:rvnSystem76,Inc.:rnLemur:rvrlemu6:cvnSystem76,Inc.:ct10:cvrN/A:
dmi.product.name: Lemur
dmi.product.version: lemu6
dmi.sys.vendor: System76, Inc.
version.compiz: compiz 1:0.9.12.2+16.04.20160526-0ubuntu1
version.ia32-libs: ia32-libs N/A
version.libdrm2: libdrm2 2.4.67-1ubuntu0.16.04.1
version.libgl1-mesa-dri: libgl1-mesa-dri 11.2.0-1ubuntu2
version.libgl1-mesa-dri-experimental: libgl1-mesa-dri-experimental N/A
version.libgl1-mesa-glx: libgl1-mesa-glx 11.2.0-1ubuntu2
version.xserver-xorg-core: xserver-xorg-core 2:1.18.3-1ubuntu2.2
version.xserver-xorg-input-evdev: xserver-xorg-input-evdev 1:2.10.1-1ubuntu2
version.xserver-xorg-video-ati: xserver-xorg-video-ati 1:7.7.0-1
version.xserver-xorg-video-intel: xserver-xorg-video-intel 2:2.99.917+git20160325-1ubuntu1
version.xserver-xorg-video-nouveau: xserver-xorg-video-nouveau 1:1.0.12-1build2
xserver.bootTime: Sun Jun 26 15:38:13 2016
xserver.configfile: default
xserver.errors:

xserver.logfile: /var/log/Xorg.0.log
xserver.outputs:
 product id 1202
 vendor LGD
xserver.version: 2:1.18.3-1ubuntu2.2