We had a look into the "not responding" issue, but are unable to reproduce this on our Ubuntu machines. We think it is caused by the game loading the necessary resources at startup and some Linux distributions triggering this dialogue very aggressively. We already do the loading asynchronously, so we don't really know why Linux thinks it is not responding.
Thanks for looking into this.
After doing some further research: It appears to be a common issue in GNOME that this dialog shows up if an application is busy for some seconds and does not respond quickly enough. Since there are several complains, this may subject to change in other versions of GNOME.
If you're interested, you could reproduce this using a Debian live image in the GNOME flavor and start RotT in there. However, I wouldn't care too much if this doesn't affect a majority of Linux users.