ok, we have solved most of the issue, by going into items and changing the menu associated with the itemid. I'm not sure why this is necessary, it seems that we are doing this quite often on various areas of the site. Also we have made many urls "non-sef" so that they do not process in the system.
We still have issues with cache. Sometimes when we delete cache, or purge cache from ArtioSEF, then go to tools and do joomla cache and purge expired, things still do not refresh properly. I am thinking now to completely turn off artioSEF cache and just use joomla cache.