Hi there,
We have just had the same problem, been with Shopify around 3.5 years and never had this issue, always had weekly payouts running Wednesday to following Tuesday and paid out on the Friday after. Never had an issue, always been paid 100% of our balance.
I talked with the help centre earlier and they said initially said it was due to a chargeback, we have not had any chargebacks they then confirmed this. They then said it was due to the cut-off for the payout, however, today is Sunday and we are between our usual Wednesday-Tuesday, which they then also confirmed. So the final explanation was that it would just get added to my next payout after this one. It makes no sense, I am a little cautious to continue taking sales etc. with Shopify.
Did either of you get a resolution to the same issue? Have you had the same issue since?