java based applications have derped up window decorations.

[poetzmij]

Any Java app, in any JRE has a messed up window border(decorations? I don't know). They seem to be almost misaligned, they are not movable, close-able, minimize-able with window controls. though they can be maximized with the good old alt+mouse drag to the top which also corrects the issue. I've attached a screenshot with visualVM experiencing the issue. This leads me to believe it isn't java at fault and that it is indeed probably compiz, this began right after an update and restart process in which compiz was updated.

So main points are:
Windows are not showing some content at the top as if its behind the decoration, leaving blank area at the bottom.
Windows are not movable unless using alt-mouse drag on the whole window.
Window controls sometimes aren't visible and when they are they cannot be clicked.
Maximizing the window with alt-drag to the top allows all content to be seen, and pulling out into a regular window again corrects the issue until the java app is reopened.
I think it is compiz at fault, as I have tried multiple JREs and apps. It was also right after a compiz update.

ProblemType: Bug
DistroRelease: Ubuntu 13.04
Package: compiz 1:0.9.9~daily13.03.01-0ubuntu1
ProcVersionSignature: Ubuntu 3.8.0-9.18-generic 3.8.1
Uname: Linux 3.8.0-9-generic x86_64
NonfreeKernelModules: nvidia
.proc.driver.nvidia.gpus.0: Error: [Errno 21] Is a directory: '/proc/driver/nvidia/gpus/0'
.proc.driver.nvidia.registry: Binary: ""
.proc.driver.nvidia.version:
 NVRM version: NVIDIA UNIX x86_64 Kernel Module 310.32 Mon Jan 14 14:41:13 PST 2013
 GCC version: gcc version 4.7.2 (Ubuntu/Linaro 4.7.2-22ubuntu2)
.tmp.unity.support.test.0:

ApportVersion: 2.9-0ubuntu2
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
Date: Fri Mar 1 22:11:56 2013
DistUpgraded: Fresh install
DistroCodename: raring
DistroVariant: ubuntu
DkmsStatus:
 nvidia-310-updates, 310.32, 3.8.0-8-generic, x86_64: installed
 nvidia-310-updates, 310.32, 3.8.0-9-generic, x86_64: installed
GraphicsCard:
 NVIDIA Corporation GF108 [GeForce GT 425M] [10de:0df0] (rev a1) (prog-if 00 [VGA controller])
   Subsystem: Dell Device [1028:0468]
InstallationDate: Installed on 2013-02-27 (2 days ago)
InstallationMedia: Ubuntu 13.04 "Raring Ringtail" - Alpha amd64 (20130227.1)
MachineType: Dell Inc. XPS L401X
MarkForUpload: True
PackageArchitecture: all
ProcEnviron:
 PATH=(custom, no user)
 XDG_RUNTIME_DIR=<set>
 LANG=en_US.UTF-8
 SHELL=/bin/bash
ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-3.8.0-9-generic root=UUID=34cacb30-28a3-4f33-9e14-064283d07c83 ro quiet splash
SourcePackage: compiz
UpgradeStatus: No upgrade log present (probably fresh install)
dmi.bios.date: 12/22/2010
dmi.bios.vendor: Dell Inc.
dmi.bios.version: A06
dmi.board.name: 0KXFG0
dmi.board.vendor: Dell Inc.
dmi.board.version: A00
dmi.chassis.type: 8
dmi.chassis.vendor: Dell Inc.
dmi.chassis.version: Not Specified
dmi.modalias: dmi:bvnDellInc.:bvrA06:bd12/22/2010:svnDellInc.:pnXPSL401X:pvrNotSpecified:rvnDellInc.:rn0KXFG0:rvrA00:cvnDellInc.:ct8:cvrNotSpecified:
dmi.product.name: XPS L401X
dmi.product.version: Not Specified
dmi.sys.vendor: Dell Inc.
version.compiz: compiz 1:0.9.9~daily13.03.01-0ubuntu1
version.ia32-libs: ia32-libs N/A
version.libdrm2: libdrm2 2.4.42-0ubuntu1
version.libgl1-mesa-dri: libgl1-mesa-dri 9.0.2-0ubuntu1
version.libgl1-mesa-dri-experimental: libgl1-mesa-dri-experimental N/A
version.libgl1-mesa-glx: libgl1-mesa-glx 9.0.2-0ubuntu1
version.nvidia-graphics-drivers: nvidia-graphics-drivers N/A
version.xserver-xorg-core: xserver-xorg-core 2:1.13.2-0ubuntu2
version.xserver-xorg-input-evdev: xserver-xorg-input-evdev 1:2.7.3-0ubuntu2
version.xserver-xorg-video-ati: xserver-xorg-video-ati 1:7.1.0-0ubuntu1
version.xserver-xorg-video-intel: xserver-xorg-video-intel 2:2.21.3-0ubuntu1
version.xserver-xorg-video-nouveau: xserver-xorg-video-nouveau 1:1.0.6-0ubuntu3
xserver.bootTime: Fri Mar 1 20:29:19 2013
xserver.configfile: default
xserver.errors:
 open /dev/dri/card0: No such file or directory
 open /dev/dri/card0: No such file or directory
 open /dev/fb0: No such file or directory
xserver.logfile: /var/log/Xorg.0.log
xserver.outputs:

xserver.version: 2:1.13.2-0ubuntu2

[poetzmij (poetzmij)]

This is minecraft showing same issue, running in openjdk JRE. VisualVM was running in oracle JRE.
Window controls are visible but unusable. Just proof of the issue across multiple apps, and JREs.

[Launchpad Janitor (janitor)]

Status changed to 'Confirmed' because the bug affects multiple users.

[J (jsartti)]

Confirmed fixed in compiz 0.9.9~daily13.03.06-0ubuntu1 for me.