Intellij Idea works differently when started from Cairo Dock

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)