Zotero 4.0.27.2 is out now with the fix for secondary toolbars (or at least the Bookmarks Toolbar) on OS X and Windows. A Linux fix is forthcoming. I'll also take a look at some other non-standard configurations — e.g., themes and vertical toolbars — when I have a chance. If something still looks off in one of the standard Firefox locations without modifications, let me know.
Sorry for the late reply but I've only just updated having been travelling for the last month or so. I'm in a similar situation to francisjhpark in that I use Classic Theme Restorer and use small icons and have a large icon where the icon is too large and the image takes up the whole icon. The weird thing I notice that if I use normal size icons the icon image is now the right size although the button itself is now larger (as you'd expect with normal size buttons). Does this help in finding where the problem is? I can provide a screen shot if it would help.
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@namespace url(http://www.mozilla.org/keymaster/gatekeeper/there.is.only.xul);
@-moz-document url-prefix('chrome://') {
toolbar[id="nav-bar"] #zotero-toolbar-save-button-single .toolbarbutton-icon {
width: 22px !important; /* Compensate for border on only one side */
}
}