I have had the same issue... This is a longer fix, but its all that will work at this point as when QB downloads bank transactions, it also downloads a specific ID# XXXXX prevent duplicates and that same safeguard is what is causing you the problem now. I know it doesn't feel like it at the moment, but believe me, this is a better problem to have than what QB used to do when it would download duplicates... (That was a mess!)
Your download should be a .qbo file? If so, open it in a text editor (there's one installed called TextEdit or you can use Word) and have a look at it. You should be able to make out transactions - any file with a lot of transactions will go on for several pages.
If you don't see any transactions the problem is the download from the bank.
If you do see transactions, are they already entered in QuickBooks? Perhaps in a different bank account? Each transaction includes a TRANSID - a unique identifier that forever represents that transaction (if you download it from the bank again you'll see the same TRANSID).
Try this (at least for Quickbooks 2011 MAC):
1. Go to your chart of accounts, select the account you're having issues with and click on "Edit Account".
2. Now click "Online Settings", at the bottom select the dropdown "Downloaded transactions" and change it to "Not enabled".
3. Download the data via Quickbooks web connect from your bank using only the dates that you need, don't go back further or you'll have to manually match transactions.
You should now have a .QBO file, open this in text editor.
4. Scroll down till you see "<ACCTID> " and you should see your account number / CC number after that.
5. Now delete the last digit of your account number.
6. Now import your file and select the account you want it associated with.
The next time you import your data, you'll first have to go back through steps 1 & 2 above.
But this time DON'T delete one of the digits on the account number with text editor.
You'll have to again select the account the data belongs with and then you should be back on track.