Did you ever get this resolved?  I am having the same issue...I'm processing sales receipt orders, the customer credit card apparently gets charged and the receipt shows PAID.  But when I go into my QB deposits, the payments are not showing up (some are, not others).  When I go into sales transactions, the orders show paid.  The money is also not showing up in my bank account.  QB tells me this is because those particular charges show up on their back end and are "in review".  I reached out to a couple of my customers who I have long-term relationships with and they tell me their credit card companies are not showing any charges from my business whatsoever.  I am SO frustrated.