I added a check for widget type in git so that focus is drawn only if the widget is GtkCheckButton (or derived). This disables focus drawing of the option/check for every other widgets than GtkCheckButton and GtkRadioButton, and thus in tree/list view it's not focused.

I pulled the latest git and compiled it, and the originally described problem does not seem to have gone away.

Any chance you forgot to ./configure with --prefix=/usr? I compile/install through rpm and this issue is fixed for me (well, I tested it only in cvs snapshot of gajim).

Just tested it, to be sure, in Package Manager as well, and the problem does not appear there either.

I used ./autogen.sh --prefix=/usr, and for me the problem appears both in Package Manager and in Pidgin.

That's really strange. The only thing I could think of is that the new library wasn't loaded by the applications. Could you try installing it via rpm and then restarting the package manager/pidgin? SRPM is here:
http://mso.fedorapeople.org/nodoka/gtk-nodoka-engine-0.6.99.1-0.8.git.0995907.fc8.src.rpm

Why has the property "indicator-size" no effect on the checkboxes in a treeview with Nodoka?

And why are the checkboxes not centered with Nodoka?

Here are screenshots:

http://people.redhat.com/twoerner/tmp/s-c-fw-Clearlooks.png
http://people.redhat.com/twoerner/tmp/s-c-fw-Nodoka.png

After logging out and restarting the gtk application, the highlight problem is solved for me, but the other problems (see above) are still there.

Replying to [comment:8 anonymous]:

Why has the property "indicator-size" no effect on the checkboxes in a treeview with Nodoka?

Because we use fixed size, like is used in the murrine engine IIRC, from which Nodoka is a fork. If you'd like to have it, please create a separate bug for it.

Replying to [comment:9 anonymous]:

And why are the checkboxes not centered with Nodoka?

This is most likely a bug and it might be worth investigating. I quickly checked on my F8 box, and from the engines I tried only nodoka has it centered, so there might be some changes in s-c-fw or the widgets its using which fixed the behaviour for clearlooks, mist etc. but broke for nodoka. Please file a separate bug about it.

Replying to [comment:11 anonymous]:

After logging out and restarting the gtk application, the highlight problem is solved for me, but the other problems (see above) are still there.

OK, so closing this bug as the other problems should be handled separately as they are different problems than this bug is addressing.

I forgot to log in... so the three previous comments are from me...