Created attachment 1748 [details]
Screenshot with the error messages

HOST: Ubuntu 13.10
poky: 1a9226f140f578f11696abf1a3c989fae1d4c14a
eclipse-poky-kepler: c73c6e4510c42601854f3c542ca6e14b4510380c
eclipse-poky-juno: 26bfc407781aa185f244a47ba63120343cee4a37

STEPS TO REPRODUCE
1. Install Eclipse using the Headless Build
2. Set the Yocto ADT's toolchain, sysroot location and kernel
3. Launch a QEMU from Eclipse
4. Create a new C/C++ project
5. In the Project Explorer window, right click the project -> Reconfigure project
6. In the Project Explorer window, right click the project -> Build project
7. In the Project Explorer window, right click the project -> Run as -> Run Configurations
   7.1 Under Run Configurations expand "C/C++ Remote Application". A configuration for the current project should appear. Clicking it will display the configuration settings.
   7.2 in "C/C++ Application" field input Remote Absolute File path for C/C++ Application. e.g.: /home/root/myapplication
   7.3 In "Connection" drop-down list make sure a SSH connection is set up for your target. If not, create a new one by clicking the New button.
   7.4 After all settings are done, select the Run button on the bottom right corner

8. Close the QEMU opened at step 3
9. Open another QEMU from Eclipse which has the same IP like the QEMU that had been closed at step 8
10. In the Project Explorer window, right click the project -> Run as -> Run Configurations
   10.1 Under Run Configurations expand "C/C++ Remote Application". A configuration for the current project should appear. Clicking it will display the configuration settings.
   10.2 in "C/C++ Application" field input Remote Absolute File path for C/C++ Application. e.g.: /home/root/myapplication
   10.3 In "Connection" drop-down list make sure a SSH connection is set up for your target. If not, create a new one by clicking the New button.
   10.4 After all settings are done, select the Run button on the bottom right corner

EXPECTED RESULT 
Run succeed and the console outputs "Hello world"

ACTUAL RESULT 
Two pop-up error windows appear as you can see in the attached screenshot.
The error from the first one is : Connect to "IP" was canceled
The error from the second one is : Error doing file upload: Operation failed: File system input or output error

If after step 8 the Remote System Explorer Perspective is opened the bug doesn't reproduce anymore.