Using JA_Transmenu in Legacy mode on Joomla 1.5. Looks like the core SEF and Joomla are not working correctly together.
When SEF enabled with mod_rewrite off, I get the the section/category added before the index.php thus resulting in error 404 or 500 when clicked.
Eg. http://www.xxx.com/services–overview/portal-architecture/index.php/services–overview/product-migration/73.html
instead of
http://www.xxx.com/index.php/services–overview/product-migration/73.html
Currently not enabled on site, because it breaks it, but basically all links are incorrect. Once Transmenu is off, the links generated are fine.