I am having this too. It started happening about 2 months ago and has not been resolved. I spoke with tech support and they just had me reset data and try again. Well that didn't solve the issue. Manually downloading txn's results in duplicates of all the main card txn's and is not a workable solution.

What is going on? If QBO can't get this right there is no reason for me to stay with QBO since there are a lot of other accounting solutions that will work with manual downloading txn's.