I haven't been able to find anyone else with this same problem via google.
I run a number of medium-large sites with joomla 3 with joomsef and i have noticed that on a lot of the urls, end with ?view=******
e.g clicking on a normal menu link for Chronoforums2 the url is displayed /forum?view=board though this happens with other components as well when clicking from a menu link I have the same issue with chronoform links as well.
I have spoken with the gang at chronoengine and they don't know what is causing it and doesnt think it has anything to do with their packages.