After a lot of testing, I finally figured out what is causing the "visualizedirtregions" to trigger. In the Keymap editor addon I have a keymap for deleting files. This always worked fine but apparently since my switch to Libreelec, pushing this button triggers the CTRL + SHIFT + R command whichs activates the "visualizedirtregions". In Openelec 6.0.3 I never had this issue. I'm going to do some further testing to see if I can define the keymap in another way.
Edit: I just found out that it is not the Delete command which is causing the issue, but the specific button that I'm pressing on my Logitech Harmony remote. I was pushing the red button, which is sending a "red" command to the Kodi device. Apprantly the red command is triggering the "visualizedirtregions" in Libreelec but not in Openelec.