So, since you are using WebConnect, you have the .qbo file. Open that in text editor and find the transaction that isn't being imported. You can change the FITID for that transaction to something different (make it wildly different - like add 7777 to the end of it) and try importing the qbo file again. If the transaction now comes in the issue is the original transaction id.
The question then is whether you've already added that transaction to the register or if you've marked it for deletion. In either of those cases QB is working as designed. It has to do this to prevent duplicate entries and ignoring your commands to delete a transaction.
The more insidious case is if the bank isn't marking the transactions uniquely. In order to determine that you have to search all your .qbo files and see if that transaction id has been used previously in one of them. Spotlight can search them so just typing the transaction id in Spotlight may tell you - if you've kept all your old .qbo files and haven't deleted them.
