This has been a recurring, but inconsistent problem, after Quicken updates. A checking account that I haven't used in several months that should have a zero balance suddenly showed a negative $150K balance. I traced the problem to over 5 years of my income transactions inside that account. These were entered as splits, not using the paycheck form. In all these transactions, the signs were reversed on all the split amounts inside the transaction. I had to manually go into each transaction and use the 'adjust' button to get the transaction to show the correct signs and amount deposited.
This has happened only after a software update, but not every time and not every account. It's very frustrating.
I'm on Win 11, R66.28.