@gaz I am out of ideas here, and having never used the Lightgun outside of the Raspberry Pi, I would definitely suggest bringing this back to the Sinden Lightgun discord, as Andy will likely be able to best help troubleshoot the scenario.
Specifically, if the gun works in other software such as the test apps, it might be something simple that I am not knowledgeable enough nor experienced enough to detect. The Linux-specific channel there might be the best to get to the bottom of this, but do share whatever you find here, as if there's something that we can change on our end I suspect we'll be happy to accommodate.
Sorry about that.