This is the wierdest thing i see playing civ, playing on huge earth map, middle of industrial age, im at war with certain country and everything is ok, untill i conquer one of their cities, it lets me select what to build in that city, then when i quit the city screen civ freezes for ~5mins, and when it unfreezes all enemies cities are destroyed except one with population 1, is there anything to do about this?

Sounds like you have Elimination turned on as a victory condition.

Do you have a before and after save?

Yep before and after, but before that i was engaged in 2 other wars, conquered cities and everything was ok, what elimination does?

Elimination is a VC introduced in PTW and present in C3C where if you lose one city, you lose them all. In Conquests you can change the threshold from 1 to 10, but in PTW it's set at 1.

If you're taking enemy cities before this, then you don't have elimination turned on. U/l a save, and we can look at it.

I've checked score screen, it was elimination, with city limit 10, damn wasted about 10hrs playing that map.

Ah, well. Now you know.