Welcome to the forum!
When you see the white box around the logo, where do you see it? Is it in the EPS file that's open with Inkscape? Or are you looking at the EPS in a browser or some other viewer?
I'm not set up to handle EPS files, so I can't look at your file to figure out what might be wrong. But if you could make a screenshot of the white box, that might help.
Or else you could share the EPS file, and someone else might be able to look at it.