Public bug reported:

[I'm not sure against which package I can report this, so I've
preliminary done it against `qemu`]

Since I have a non-standard keyboard (a Kinesis, without Super key), I remapped 
a key on my system (XUbuntu 16.04).
This is accomplished via:

    ~$ cat ~/.Xmodmap
    keycode 108 = Super_L

This works fine, but after any qemu execution, with passthrough of my
USB keyboard, the mapping is lost - more precisely, the system it starts
behaving like the key is not mapped.

ProblemType: Bug
DistroRelease: Ubuntu 16.04
Package: qemu 1:2.5+dfsg-5ubuntu10.2
ProcVersionSignature: Ubuntu 4.4.0-31.50-generic 4.4.13
Uname: Linux 4.4.0-31-generic x86_64
NonfreeKernelModules: zfs zunicode zcommon znvpair zavl
ApportVersion: 2.20.1-0ubuntu2.1
Architecture: amd64
CurrentDesktop: XFCE
Date: Thu Aug  4 19:11:24 2016
EcryptfsInUse: Yes
InstallationDate: Installed on 2016-07-11 (24 days ago)
InstallationMedia: Xubuntu 16.04 LTS "Xenial Xerus" - Release amd64 (20160420.1)
KvmCmdLine:
 COMMAND         STAT  EUID  RUID   PID  PPID %CPU COMMAND
 kvm-irqfd-clean S<       0     0  1261     2  0.0 [kvm-irqfd-clean]
MachineType: Gigabyte Technology Co., Ltd. To be filled by O.E.M.
ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-4.4.0-31-generic 
root=UUID=7f35da3f-4f3a-40e1-8af0-3f02cfbf9884 ro
SourcePackage: qemu
UpgradeStatus: No upgrade log present (probably fresh install)
dmi.bios.date: 12/24/2015
dmi.bios.vendor: American Megatrends Inc.
dmi.bios.version: F6
dmi.board.asset.tag: To be filled by O.E.M.
dmi.board.name: F2A88XN-WIFI
dmi.board.vendor: Gigabyte Technology Co., Ltd.
dmi.board.version: x.x
dmi.chassis.asset.tag: To Be Filled By O.E.M.
dmi.chassis.type: 3
dmi.chassis.vendor: Gigabyte Technology Co., Ltd.
dmi.chassis.version: To Be Filled By O.E.M.
dmi.modalias: 
dmi:bvnAmericanMegatrendsInc.:bvrF6:bd12/24/2015:svnGigabyteTechnologyCo.,Ltd.:pnTobefilledbyO.E.M.:pvrTobefilledbyO.E.M.:rvnGigabyteTechnologyCo.,Ltd.:rnF2A88XN-WIFI:rvrx.x:cvnGigabyteTechnologyCo.,Ltd.:ct3:cvrToBeFilledByO.E.M.:
dmi.product.name: To be filled by O.E.M.
dmi.product.version: To be filled by O.E.M.
dmi.sys.vendor: Gigabyte Technology Co., Ltd.

** Affects: qemu (Ubuntu)
     Importance: Undecided
         Status: New


** Tags: amd64 apport-bug xenial

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https://bugs.launchpad.net/bugs/1609900

Title:
  After QEMU execution with keyboard passthrough, key mappings are lost

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