When converting anything into a smart object layer, the shortcut ctrl+alt+shift+t produces inconsistent and unrelated (to what was the transformation) results. This was verified by other Photoshop users on the Adobe forum.
Lukasz & Jaroslav: So sorry you're running into this. We do already have a bug on this behavior and we're going to be looking into it, though I don't have any concrete information for you right now. Thanks for raising this issue. -Eric FlochPhotoshop Quality Engineering