Hey there @fwilleke80 and @m_magalhaes
Thanks so much for your responses!
The 'code' is an expression tag. Expression tag reacts to a User Data switches on some Null object. Switches make different sets of Instance objects become visible or invisible.
At the end of the project I create Takes, each take has recorded a click on UserData Button. This click makes expression tag code to show/hide different instance objects. The geometry is heavyweight, so it takes a couple of seconds for C4D to make these instances visible.
If I export each take to a separate scene or if I select takes manually - each render shows corresponding set of instances. But on batch render every take shows the same geometry from the first take, as it has not enough time to switch instances, before the render begins.
I am not sure if it's possible to discuss this problem without showing the actual code (it's around 2000 lines).