After Upgrading to SOAP UI 5.6.0 some windows on the right side will no longer close, including the Start Page. When you click the 'X' the window becomes empty, but does not close. Only option is to minimize and it stays there until you restart the program.
You can prevent start page to open every time by changing setting as below:
Go to Prefrence -> UI Settings then uncheck "Open Startup web page when starting SoapUI" :
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That may work for the start page, however other windows that I open to run some tests are subject to the same issue and will not close. I have not been able to link to a specific action or use as of yet.