Firstly, you might try not using the vinegar in the final rinse. Often it helps with softness, but it sometimes can contribute to smelly dipes.
the other important thing is to make sure your dipes don't have detergent build up. Wash and rinse until the water runs clear and then just use as little detergent as you can to get the diapers clean.
I use Bio-Kleen on ours and ended up skipping the baking soda and vinegar altogether as it didn't really help with stains and our water already produces nice, soft diapers.
First do a cold soak and wash or rinse.
Then do a hot wash. It's really important to do one of these to get things really clean and non-smelly in my experience.
Another cold rinse (you could put in a fe w drops of essential oil if you like).
I put them in the dryer for 20 mins and then hang to dry.
It has worked really well for over a year now.
Some people use their washing machine as their diaper pail and just soak straight away. To my mind that is ideal because it will really eradicate staining and smells, but its not practical for me.
Additionally I wouldn't use vinegar with those diaper covers that you mentioned.The manufacturers say that it doesn't affect water proofness, but I have heard anecdotal evidence to the contrary. They can just be washed with clothing or quickly hand washed and dry pretty quickly.
HOpe some of this is helpful. Sorry if I have repeated anyone. My toddler woke up and has been put back to sleep halfway through my reply!