What is wrong with the reference function?
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It's not clear to me what the original poster is talking about - I'm not convinced the original poster is sure either.
In my experience: there is nothing wrong with the "Reference" column (and, the Reference column is not a Quicken "function").
In Checking and Savings accounts, there is a dropdown list in the "Check#" column. That dropdown list contains choices supplied by Quicken, and allows the user to add choices of their own. One of the choices supplied by Quicken is TXFR. This is ONLY true for Quicken checking and savings accounts.
When TXFR is entered in the Check# field in checking and savings accounts, Quicken will require a "transfer category" (a Quicken account name in square brackets) in the Category field.
In other Quicken non-investment accounts (such as - but not limited to - credit card accounts), there is a "Reference# column. That column can contain any text the user wants to enter - but no entries in that column are "remembered" by Quicken, there are no Quicken supplied values for the Reference#, and there is no dropdown list for the Reference# where Quicken users can add values for Quicken to "remember".
If the user wants something in the Reference# field, they will have to manually enter it ... every time they enter a transaction.
Also: it is never necessary to have "TXFR" in the Check#/Reference# field in order to enter a transfer transaction (in order to enter a transaction with an account name in square brackets in the category field). In other words: it is ALWAYS possible to enter a transfer category in the Category field of a Quicken transaction - regardless of the contents of the Check#/Reference# field.