Hello,
we are preparing a new version of JoomSEF to be published during this weekend or in the beginning of the next week.
This version will introduce a new option which enables you to ignore the link source (the ItemID parameter in the URL). This way you will not get any duplicate links to a certain target, even if they come from different sources (menu, link, bottom menu, ...). Of course that has also drawbacks -- the behiavour of Joomla may not be what you want -- the menus may not change according to where you come from, etc. (that is what the ItemID is used for)
But at least, you will be able to choose what you prefer.
If anyone has some ideas/wishes to this topic, please mail them asap to
info@artio.cz.
Best regards,
Michal