I also have hundreds of auto-match transactions I have to work through each month. I found the issues comes up most often with transactions I had to add manually because they were dropped in he bank feed. QB tends to drop transactions that had the same amounts from the same vendors. This happens to me monthly with many transactions. So when I go in and add the expense manually, each month it tries to auto-match that manual transaction to the manually added one. The auto-match flaw is that it doesn't take the date into account. As someone said above, it takes the amount and vendor name. This is supposed to be a time saving feature, but it instead does the opposite. I spend many hours (usually unbillable time) trying to work around this issue. It just gets worse each month . I'm currently looking at 211 auto-matched transactions I have to deal with and I'm so angry! This feature should have been fixed a long time ago. It should have a select all and un-match all button. Or just turn it off all together!
