Are you making the exploded lines in your model or your drawing?
It has been my experience that you cannot have individual exploded views for each configuration.
This alone may be your issue. If you place the lines perfect for one config and then switch to the
next one, the lines are probably confused because either the part moved or is not longer there.
Do you have the exploded distances controlled in your configurations?
Are you using a designt table to control the configs?
I am using these lines in my model. I have been doing this for years with earlier versions of Solidworks . I always created different configurations to my assembly models then from that I created different drawing sheets, no issues. I am not using any design tables.