Difference in running testrunner standalone or from within the tool

I want to understand the difference in running the soap ui test runner.bat from command line or from Test Maker versus running it from within the Soap UI tool.

The reason is, I have script assertions which writes the results to a log file. It creates the log file which I run the test case from within the tool. but when I invoke it from command line or from test maker tool, it does not execute the script assertion and does not produce the file.