OK, I think I know what you're talking about.
In my case, I have an auto-invest setup at Vanguard.
They initiate an EFT withdrawal from my bank then they do the BUY.
The BUY is added as a debit in my Vanguard cash (Money Market) account, which is resolved when the EFT is posted.
Next, it goes through what I've heard called the sweep to balance the account.
When the transactions are downloaded by MD, the funds I transferred via my checking account are reported back as cash. I cannot find a way to have that associated with the EFT to Vanguard. Hence a duplicate transaction.
Sorry, I've had no luck figuring it out. Perhaps another user has a suggestion.