Hi Ray,
I’m currently having the same issue, so naturally, I went searching and found this post.
I know its a while since your post, but I found the reason my payouts are significantly less compared to total sales… I hope you’re sitting down.
Shopify has not been payout out the taxes and shipping revenue charged to my customers. They’ve been paying out the pre-tax amount for the products only.
So far, I have found they owe me and my business approx AUD$30,000.
Now the fun part begins. They’re claiming that the “Shipping Revenue” is actually shipping charges, which I fully dispute because I receive separate bills if I create a shipping label in Shopify (I no longer do this, but at the time, I was).
They’re also claiming to pay the tax on my behalf to the Australian Tax Office. However, this is nearly impossible because they do not have my Aust. Business Number. They also don’t know how much to pay…
Funny isn’t it… they got caught, and I’ve proved it several different ways… but they’re still fighting!
I hope you don’t have the issues anymore, but if you do, I hope this helps.