I was able to reproduce this on Ubuntu 20.04 LTS. Digging into this more, it looks like the issue with the panel overlapping other windows on Linux has been around for a while: Bug 1439609. The **browser.download.improvements_to_download_panel** preference made this issue more apparent since it now opens the panel when there are no other downloads in progress. I believe we added an option to turn this off in Bug 1738372. You can go to about:preferences and set **browser.download.alwaysOpenPanel** to false, which would bring back the old behaviour of the panel.
Bug 1741076 Comment 4 Edit History
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I was able to reproduce this on Ubuntu 20.04 LTS. Digging into this more, it looks like the issue with the panel overlapping other windows on Linux has been around for a while: Bug 1439609. The **browser.download.improvements_to_download_panel** preference made this issue more apparent since it now opens the panel when there are no other downloads in progress. I believe we added an option to turn this off in Bug 1738372. You can go to about:preferences and set **browser.download.alwaysOpenPanel** to false, which would bring back the old behaviour of the panel. I'm going to mark this as resolved since we have the **browser.download.alwaysOpenPanel** preference in place now, but feel free to re-open if you're still seeing the same issue.