I am having the same problem. I checked the Make Deposit window and the date and account are correct. But the deposit does not show up in the check register or, of course, the reconcile screen.  I recently reinstalled QB because I have a new computer. Do you think there could have been some glitch in the install?  This is the only problem I have had and I am baffled because this is the same procedure I have used for many years with no such issue.   Thank you for any advice.