I was experiencing this issue on OSGeo Live, which uses Xubuntu.

I have followed instructions and set the unclutter settings as follows:
```
EXTRA_OPTS="-idle 2 -root -noevents"
```

Running the following command resolved the issue:
```
unclutter -idle 2 -root -noevents &
disown -h
```

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https://bugs.launchpad.net/bugs/1255507

Title:
  Running unclutter without "-noevent" causes focus problems for Firefox
  and Thunderbird

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