URL problems after migration to CP3

I migrated from Custom Properties 2 to the latest CP3 because of Joomla migration from 2.5 to 3.3.

On 'Custom Layout' menu item I have listed some articles.

When I clicked an article in CP2 version I was directed to url formed like this:
In CP3 version I noticed a shortened url after clicking an article:
Is there any way I can retrieve back old formed urls (longer ones)? I am using two different templates in my page. First one is for homepage and second one is for other pages. Problem is, my first template applies (only in CP3 version) for all articles as well if I access them from shortened url-s (articles should use my second template).

Shorter URLs ("SEFized" urls) are created by Joomla when a menu item pointing to that article (or to the article's category) exists.

Longer URLs are used otherewise.

I'm inclined to believe that you created some new menus and menu items in your new J3.x site that in turns make some older non SEF URLs into SEF ones.

I have not changed anything after migrating Joomla to 3.3. I only install new CP extension and update all menu item types to "Custom Property Layout" again. It is possible that change happened due to new Joomla 3.x and not CP extension itself. I will try to find answers on official Joomla forum as well.