Problem with Account Balances Report - balances way off!

I was looking at why my Net Worth figure listed at the bottom of the sidebar is so different from what is listed in the Net Worth panel under Property & Debt. I clicked the Account Balance report and found that a bunch of my accounts have erroneous balances.

For example one of my main checking accounts has a huge negative balance where it doesn't show that in the normal transaction list for that account. And two of my brokerage accounts which are now closed and zeroed out are showing negative balances. They have a huge negative "cash" balance and are showing that I have a negative balance on a particular security. When I try to go into that account and look at the holdings, it says that holding doesn't need to be set to zero. So I am not sure where the discrepancy is coming from.

I already tried to validate my file, which didn't fix it, and tried to super validate it, which also didn't fix it.

Any suggestions?