When creating a "link to a file or website" resource from Internet Explorer, if the option to have the link open in a new window is selected, the sub-options that are checked by default (such as enabling scroll bars and window resizing) do not actually remain checked after saving. (After initially creating the resource, if the teacher goes back to edit it and manually checks the options, they do remain checked.)
I can reproduce this behaviour every time using either IE7 or IE8 (do not have an IE6 to test with) and with two different installs of 1.9.4+ Build 20090401. Tried different themes just in case, but that did not change the behvaiour.
I cannot reproduce the problem from an install of 1.9.4+ Build 20090204 nor on demo.moodle.org (which is Build 20090209 at the moment). The problem does not occur when creating the resource in Firefox.