I have the same problem as ckrosco does. I did some testing and it actually seems to be a fairly serious problem. What I can do, enter a payment for a customer but his payment leaves a balance. All is fine, he owed for several invoices. Then click 'enter another customer payment'.
That screen stills shows the last customer, so I hit space, enter a new customer for his payment. The customer comes up as does his branch. Then enter an allocation (don't even look at the amount of the balance) just enter an amount, hit 'add payment'. Get the next screen saying 'payment successfully entered'. This all sounds great except the last payment I entered was actually posted to the first customer, not the second. I tested this several times and when the search for customers is turned on it aways will post to wrong account. With the search for customer off, I could not cause it to happen.
If I do payment for cust1, go to 2nd and not add but go to 3rd customer, the back to 2nd, the error does not happen.
It seems to me that when I click 'enter another customer payment', I should get a clean screen not one that shows the previous customer's info. Even if I click Sales then customer payments the last customer still comes up.