Yepp, your guessed, what's happened... That's also originated in malfunctioning of the latest Artio. I had originally both section/category stuff turned on. Switching to the latest Artio fucked it up, because the schema is used only for generating section.and/or category based urls, not for the inner pages, to be clear:
www.mysite.com/mysection/mycategory/ is generated correctly
but instead of
www.mysite.com/mysection/mycategory/myinnerpage.html
latest artio generates
www.mysite.com/myinnerpage.html
I tried to play with settings, leaving only category or section to be used in URL's - this works - so URL's as
www.mysite.com/mysection/myinnerpage.html
or
www.mysite.com/mycategory/myinnerpage.html
are generated correctly for respective settings, but as side effects of experimenting I ended up with a lot of URL's as the one above picked up in mean time by users and robots alike.
Now my settings are back to the original ones (sections and categories both turned on) and Artio is downgraded to 1.2.5 to generate as possible the correct URL's.
Hope soon a fixed Artio will be out, then my problems, hopefully will be gone!