Hi,
reading the upstream bug, this seems to be related to how Cairo-Dock starts 
apps from launchers. This was changed in the latest beta / rc (3.5.99) so 
should be fixed already

** Changed in: cairo-dock-core
       Status: Confirmed => Fix Committed

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https://bugs.launchpad.net/bugs/1623012

Title:
  Intellij Idea works differently when started from Cairo Dock

Status in Cairo-Dock Core:
  Fix Committed

Bug description:
  Current state:
  When I start IDEA directly from Cairo Dock (not through Cairo Dock -> 
Applications Menu -> ...), run some Java code and try to stop it while running, 
process is not stopped (skull icon is shown instead of stop icon), and I have 
to kill it (click the skull icon).

  This happens only when I start IDEA directly from Cairo Dock, when I
  start IDEA any other way (terminal, Unity launcher, Cairo Dock ->
  Applications Menu -> IDEA) stop works fine.

  Desired state:
  Java code process is stopped without need to kill it, when IDEA is started 
directly from Cairo Dock.

  My environment:
  (I had this problem before also, with Oracle JDK and previous version of IDEA)

  Distributor ID:       Ubuntu
  Description:  Ubuntu 16.04.1 LTS
  Release:      16.04
  Codename:     xenial

  IntelliJ IDEA 2016.2.4
  Build #IC-162.2032.8, built on September 9, 2016
  JRE: 1.8.0_112-release-b343 amd64
  JVM: OpenJDK 64-Bit Server VM by JetBrains s.r.o

  openjdk version "1.8.0_91"
  OpenJDK Runtime Environment (build 1.8.0_91-8u91-b14-3ubuntu1~16.04.1-b14)
  OpenJDK 64-Bit Server VM (build 25.91-b14, mixed mode)

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