We had this same issue, and I spent hours on the phone with support just for them to tell me to disconnect and reconnect the square app.
I'm not sure if that will solve the issue going forward but it definitely won't fix all the transactions from February and March that have already come through, so I found a work around.
I noticed that the new sales tax lines coming in from square were being moved to an account called Square Sales Tax Payable instead of the correct payable account that quickbooks uses to calculate sales tax.
I took the amount that went into that account and made an adjustment to the sales tax in the review sales tax screen and put it in the Tax Expense account.
Now the total sales tax was correct, but I had to make the adjustment to the Tax expense account instead of the payable account. To fix that I also entered in a journal entry to credit the adjustment amount out of the tax expense account and debit into the Square Sales tax payable account.
Hope this helps!
example journal entry:
Square Sales Tax Payable $2000
Tax Expense $2000
