From a previous closed discussion, I found;
https://infinitekind.tenderapp.com/discussions/suggestions/809-converting-from-quicken-to-moneydance

"Split Transactions are converted incorrectly if the split includes more than one entry directed to the same category. For example, if a transaction for $100 is split $40 to the gas cagegory, $50 to the entertainment category for concert tickets, and $10 to the entertainment category for a concert program, an erroneous transaction is entered. The split transaction is entered correctly, but there will be an erroneous entry for $60 because of the two splits to the same category (entertainment). This problem should be corrected by the Moneydance developers since it is a very tedious job to eliminate all these erroneous transactions which can only be located by looking through individual account transaction registers"

Although it doesn't seem to have been resolved, I found that all the duplicates were not cleared (reconciled). Sorting by uncleared, it was easy to put all of the duplicates in one area, then select all and delete. I now have a 20 checking account that balances!