Running from the command line can cause some problems, often because you can't be sure that what you put on the command line did what you thought would do.
Ensure the arguments supplied are what you expected.
If you are testing a console application, make sure you can see it.
If an errors occur when processing the command line, make sure you can see those.
Look on the diagnostic tab to ensure the diagnostic data collected makes sense.
If you've got -hideUI in your command line, comment it out temporarily (make it -xhideUI so that it's not recognised).
If you're running from the command line, most likely you'll be running from a cmd prompt, or possibly powershell.
We've only ever had one customer report a hang with any of our tools when running from the command line.
We eventually found the problem, and it wasn't with the software tool.
The problem was that they were running the tool in hidden mode (-hideUI) from a command prompt and for unknown reasons the tool would never exit.
When they added a simple change to their command the problem went away.
They added cmd /c to the start of their command line. This opens a new command prompt and instructs it to launch the command line and wait for it to exit.
Problem command line:
"c:\program files (x86)\Software Verify\Thread Validator x64\threadValidator_x64.exe" -program c:\testProgram.exe -hideUI
Working command line:
cmd /c "c:\program files (x86)\Software Verify\Thread Validator x64\threadValidator_x64.exe" -program c:\testProgram.exe -hideUI