I tried to reproduce the issue in some different variations, but so far haven’t been able to. Having said that, I did encounter two Linux-specific issues: shortcuts with modifier keys didn’t work properly and shortcuts weren’t saved after crash.
Since there was a similar issue recently (Default shortcuts for setting ratings don't work, now fixed), I wonder if this is possibly related to the specific key combination of the shortcut. Do you have an example shortcut that didn’t work?
If neither a crash, nor a specific shortcut is responsible for this, are maybe application settings in general (e.g. the language selection) not saved?