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The original answer was not incorrect, just not the best answer. There is no need to disable the account from online access. Here is the secret way to get these transactions into Quickbooks (on Windows or Mac).
Just be sure you are bringing the downloaded transactions into the correct account. I find this issue usually occurs with credit card downloads - as in credit card accounts that have more than one credit card (eg, one master and several sub accounts) associated with them.
Here we go. First download the QBO and save the file, say, on your desktop. Right click on the file and select Open With, then choose Notepad. (on a Mac use TextEdit). Now, look thru the info listed (starting from the top) and look for <ACCTID>. It will list an account number after this. You will notice that this account # differs from what is in QB. That is what is causing the problem. In QB, from your chart of accounts right click (control+click) on the account in question, select edit account. Copy down the account number listed here. Now, type it in Notepad, after <ACCTID>, replacing what was there. Voila!! Done!. Save the file. It should save as a QBO file. Double click on the file and the transaction will flow into QB seamlessly... Matt (former online tech support for Intuit)