I think we are betting on the wrong horse here.
I can give a better example.
the notifier module both generates correct url's and incorrect url's.
My notifier contains one message. If I click on teh envelope, it generates the following correct ulr:
www.the-reflecting-circle.nl/trc/joomla/index.php/component/uddeim/?task=inbox
If I click on the message itself, in teh same instance of the noitifier, it generates the follwoing icorrect url:
www.the-reflecting-circle.nl/trc/joomla/index.php/?task=show&messageid=3
In both cases you can see that the main url of my live site is listed correctly, but the component/uddeim/ part is missing in the wrong url.
If I look at the code in the mdo_uddeim.php file, I notice the following for the CORRECT url:
www.the-reflecting-circle.nl/trc/joomla/index.php/component/uddeim/?task=inbox
is generated in line 117 by the following code:
$pms_link = sefRelToAbs("index.php?option=com_uddeim&task=inbox".($item_id ? "&Itemid=".$item_id : ""));
This link is displayed in either of three ways in lines 157-170. Example code is:
echo uddepmscalljava($message, $pms_link, $moduleSubPath);
The INCORRECT url is:
www.the-reflecting-circle.nl/trc/joomla/index.php/?task=show&messageid=3
Which is generated in line 222 by the following code:
$pms_show = sefRelToAbs("index.php?option=com_uddeim&Itemid=".$item_id."&task=show&messageid=".$themessage->id);
This is displayed in line 224:
echo "<a href='".$pms_show."'>".teaser_head($displaymessage, $maxlen)."</a>";
So I think that the sefRelToAbs function does not handle url's in the same way that the line 157-170 code does. At least, not when search engine friendly url's are used.
I hope this helps to point you in the right direction.