A workaround has been added to Clearlooks and other engines like Murrine to support programs that draw fake Gtk+ widgets (Firefox). This workaround provides a "transparent-bg-hint" that can be set to prevent the background from being drawn on entry and progress bar widgets. The intent is to fix a cosmetic defect that manifests itself as an unwanted rectangle surrounding these widgets. I've attached a patch that does a similar thing in Nodoka.
Patch to provide transparent-bg-hint in Nodoka. nodoka_transparent_bg_hint.patch
Thanks for both the report and patch :-) Looks fine so I'll add it to git later.
Fixed in git rev 057ff6f. [http://git.fedorahosted.org/git/?p=nodoka;a=commit;h=057ff6f]