I too am in this exact situation.  I probably have thousands of rules.  Some are misclassified as income instead of expenses.  So, every month I have to go through during reconciliation and find these automatched transactions and change them.  What a head ache!

The for the money Intuit charges for this software it is very buggy and it seems there could be at least a few features added to make our lives easier.

This problem should not be marked as solved!