Seriously it was just the last thing I could think of, but this should not be the reason too. In my last store, these setting were the same and payments were going through smoothly. I can guide you one thing, have you tried talking to live chat with Shopify support? please do that. I will do it too once again, and then we will share our thoughts and solutions here. what do you say?
Will talk to them now to see what action can they provide. Was thinking too if the activation of multicurrency on shopify payment affects this or what. Or does shopify fraud filter was too sensitive as I got same issue with stripe when I install the checkout X and stripe says they look for every aspect of customers information like emails, card and ip (i guess) if they did something unusual activity.