TikiWiki link permalink structure completely changed.. ..
It appears to me you may have had SEF enabled on your old version, if this is the case, simply go to your "Control Panel" then "SEF URL" and make sure that it's activated. Remember, you'll have to rename _htaccess to .htaccess before you switch to SEF URL.
I hope what I outlined above is the issue, sounds like you got a bit of a headache going there.