If you are creating page urls with extra segments like /page/subpage.aspx, that is not supported by mojoPortal. Especially if using folder based child sites it will cause problems, but even in single site installations it is not supported and has never been supported. If it worked previously it was only by happenstance not by design.
This is documented if you click the help link next to the url in page settings and also here:
http://www.mojoportal.com/search-engine-optimization.aspx
Best,
Joe