I am having a similar problem and about to lose my mind! 

I tried to run payroll on 01-Oct for 1 employee using direct deposit with QB desktop 2020 and on 03-Oct we discovered that the paycheck funds were taken out of the employee's account and then deposited back into the same account that day. I figured I messed up the payroll set up so I tried to re-run it and ran into the old "deposit-limit reached" issue. I tried contacting QB support and was told that I had set up the account correctly and to try again after 6 days after the limit resets.

6 days later: I try to re-run payroll and again get the same message.

Contacted support (after 4 hour run-around with chat nonsense) to find out that 6 days is for QB payroll online. I need to wait 14 days for QB desktop. Support lady tells me to delete the payroll and try a new unscheduled payroll. Again, same limit error.

Today is 15Oct and I tried again to run payroll. (Meanwhile, my 1 employee is about to murder me).

Same deposit limit reached error message. 

I just contacted support and received a robocall. I answer the phone and there is silence. Then I'm disconnected.

I guess I will just keep venting my Quickbook woes online until I get some support. I cannot believe they are charging monthly for this crappy "payroll" service!