There is a long-running bug in Java, mainly affecting Windows, that fails to read command line arguments with non-ASCII characters correctly.

For Jalview versions < 2.11.5.0 you will have to install Jalview in a location that doesn’t include your username, such as C:\Program Files\Jalview. This unfortunately requires Administrator privileges and will need all automatic updates to be turned off (only available in 2.11.4.0). For earlier versions you could install Jalview in C:\Temp\Jalview although this folder often gets emptied, so you may need to reinstall.

From Jalview 2.11.5.0 you (or your Administrator) will still need to install Jalview in a non-user location such as C:\Program Files\Jalview. During the installation wizard, under Advanced options, select Customise the user-space path and include a %U (per-cent, Upper-case U) in the path, e.g. C:\Temp\Jalview-Desktop\%U.

Users should now be able to launch Jalview and will get automatic updates downloaded to that folder.

From Jalview 2.12 these problems will have been resolved.