The feature (online) that compares your Quicken records to your brokerage balances has never complained, but I finally had time to dig deeper and manually compared my statement balances (and the brokerage site's balance) to Quicken. They were definitely off by around $50K or so. Not finding anything obvious in the Quicken records and trying to not be so compulsive, I decided to just reconcile the money market fund in Quicken to the value at the end of August. Quicken put in an adjusting entry and everything matches my statements. The date is incorrect because I know the mistake happened early in the year but at least I have the correct #s.
I then used the holdings comparison feature again. And Quicken STILL is happy! I'm not asking what caused the discrepancy-- I'm sure I'm responsible-- but I don't understand how Quicken could be happy with a) balances that were that far apart from the brokerage AND b) be just as happy once its own balance has been adjusted to match. Any ideas?