Agreed, but I am going to guess that the biggest problem is not the human-machine interaction, but all the hedge cases that eventually happen and require a human to make a decision. Also, consider that an outsourced analyst will probably be cheaper than building and maintaining a full fledged software solution. What you need is a good accountant who is managing few analysts so that he can intervene only when needed, saving you lots of $$ that you would spend just to have him do book keeping.

Also, a human should advise and help you to move to another bank, one that has better interfaces with modern software solutions (like the one you use or Quickbooks or the many other around).

I tell you from my experience working in finance that you will never manage bank reconciliations automatically 100%.