Run gedit ~/.gconf/apps/compiz-1/plugins/obs/screen0/options/%gconf.xml and you should see something like this:

<?xml version="1.0"?>

<gconf>

        <entry name="opacity_values" mtime="1332424921" type="list" ltype="int">

                <li type="int" value="0"/>

                <li type="int" value="0"/>

        </entry>

        <entry name="opacity_matches" mtime="1332424762" type="list" ltype="string">

                <li type="string">

                        <stringvalue>class=Ccsm</stringvalue>

                </li>

        </entry>

</gconf>

Note the first <li> in <entry name="opacity_values" ..> so that it reads <li type="int" value="100"/>. Save, log out and back in and it should be fixed.

Or you can disable the opacity plugin with one (long) command:

gconftool-2 --set --type=list --list-type=string /apps/compiz-1/general/screen0/options/active_plugins "$(gconftool-2 --get  /apps/compiz-1/general/screen0/options/active_plugins | sed 's/obs,?//')"

That will need you to log out and in again still.

Edit (this won't work for fixed-opacity windows): The default binding for increasing opacity is Alt-MousewheelUp so you could guess where the window is and try that.