In the Document properties > License if a user select "Other" and fills in a custom License URI, saves the image and reopens it in Inkscape it will keep the URI but the radiobutton for "Proprietary" will be selected. With revision r12436 comparison between licenses is done by comparing License URI and there is no way for a computer to determine if a License URI links to a proprietary license or not.
My suggestion for fix is to remove "Proprietary" and only keep the "Other" radiobutton. Though this solution got some response on IRC that it might not be a good solution cause "Other" is not a very good naming for it. Instead a different solution was suggested. (1) Rename "Proprietary" to "Unspecified". (2) If "URI License" Entry is empty the "Unspecified" should be selected. (3) If "URI License" has any text in it and it doesn't match any listed license "Other" should be selected.
More information can be found at https://bugs.launchpad.net/inkscape/+bug/372427 where the first part of this dilemma was solved.
Reproduced on Windows XP, Inkscape trunk revision 12475.