I'm using regular QB (not the online version) and I'm also having trouble. I can see that the credit card transaction was completed but it's not showing up in our check register for the bank account it went into.  When we go to reconcile the account the amount isn't there.  (Even though it IS listed if you do a search for it, but it comes up as "undeposited funds".  It is paying the invoice.

Any help you can give would be appreciated.