Couple of things...
First, do you have a front-loader or a top-loader? Front-loaders seem to be notorious for not getting dipes completely smell-free. Something about there not being enough water moving through the diaper fabric to really get all the stink out. It is ironic, since front-loaders are supposed to clean better, but apparently they don't with diapers.
Second, do you know the Ph of your water? If your water is already basic, then adding baking soda will do nothing and may make it worse. Maybe you need vinegar instead. Laundry Ph should be somewhere around 7.5 I believe. Less means it is acidic, more means it is basic. You can use the water test strips you would use for a swimming pool. Test your water as it comes into your washer, and then test it once you've added whatever you add and compare the numbers. Then adjust as needed.
Third, how many cycles are you doing? It sounds like you're only doing one with a prewash. I have to do three cycles (all with prewash)

in my front-loader (Maytag Neptune) to get my diapers smelling okay. Here is my routine:
- First cycle: cold water, longest cycle with prewash and stain cycle, extra rinse, nothing added
- Second cycle: hot water, longest cycle with prewash and stain cycle, extra rinse, small amount of detergent with a squirt of grapefruit seed extract, small swig of water softener/laundry booster, generous squirt of Bac-Out in the rinse (then I try to let them sit for long enough for the Bac-Out to really work on them before I do the third cycle
- Third cycle: remove anything that is not cotton or hemp (nylon bags and covers) then wash on hot water, longest cycle with prewash and stain cycle, extra rinse, two scoops of Oxy-Clean, vinegar in the first rinse (I have basic water)
I also dry for two cycles. If you have the option of sunning your diapers outside, that might help. I find the GSE works great to keep the stink issue down, and it was all we needed in our old house, but here we need more.
Finally, are you overstuffing your washer? I have two in diapers and even though I wash diapers every day I still have to be careful not to overload.
I hope something there is helpful. I struggle with this, too, and although my routine is intense it is WORKING and that is what matters to me. Good luck.