I am using Quick Books Online and had the same issue (marked as paid IRS payments not matching to bank transactions).

This is what resolved it for me. 

I deleted the IRS payment from Payrol Taxes --> Payment History.

Then I added it back and picked the Marked as Paid --> Synced with accounts (or something like that) option.  Before I think I picked manage outside of QuickBooks.  Once I did that I had to refresh my browser and then both bank transactions auto matched to the Payroll tax payments.