I can't believe this issue still has no resolution. I have a new bookkeeping client that has to use QBO Payroll (even though I usually advise against QBO Payroll due to glitches like this) because he does job costing with projects. Anyway, there is one paycheck (DD) that is missing from the check register even though all the other paychecks are there for the same pay period. When clicking on the Transaction journal button on the paycheck, the report just defaults to all dates instead of the debits and credits for just the paycheck. 

Since I really don't want to have to spend hours on the phone with support, I just created a journal entry that mimics the transaction journal of the employee's previous check so that I can match it to the downloaded transaction. The paycheck wasn't reflected in the financial statements anyway.