Application doesn't load in any desktop

Hi,
I am using Yosemite for a while. One application, RSA securID token application, however is behaving oddly. It worked fine until yesterday, when without any reason, every time I started it from the dock, I can see it at the Mission Control but doesn't appear in any of my 2 desktops. I've tried launching it form the Launchpad, but same behavior. I also run this command: rm ~/Library/Preferences/com.apple.spaces.plist; killall Dock; and nothing changed.
I hope someone can help me. Thanks

A screen shot from Mission Control might be enlightening.  If you can see the application window in Mission Control, what happens if you move it from one desktop to another? Or what happens if you eliminate one of the desktops?

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