Why the two systems never agree
One deposit, dozens of sessions
Insurers pay by electronic transfer (EFT), often in one deposit covering many claims. The detail of which sessions it paid for comes separately, in an electronic remittance (ERA, or 835). Industry rules allow the ERA to arrive up to three business days before or after the money (CAQH CORE), and the trace number that links them often isn't on your bank statement unless you ask your bank for it (CMS).
Payments get re-keyed by hand
In QuickBooks, payments are grouped into a deposit that has to match the bank line. When one insurance deposit covers 30 sessions, someone builds that match by hand, every time, from the EHR's reports.
Your books only see cash
EHR exports usually carry payments, not what you're still owed or what was written off. So QuickBooks shows cash coming in, while the EHR holds the rest of the picture. A busy month with slow payers can look like a loss, and nobody's sure which number is real.