Hello, I had the same issue when setting up a new environment using SoapUI 5.2.1. I have 3 different settings files with preferences for different release numbers.
Rolling back to SoapUI 5.0.0 has fixed it (we have an old env running 5.0.0 and it is working fine). Specifying the -t parameter with a setting file to use does not seem to work with 5.2.1? Or is there a config somewhere that is required for it to function properly?