The process would be easier if there was only one payment, but there must be some security or financial reason for Paypal to send you two random payments
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I suspect a 1 in 99 chance of guessing the deposit amount on a fake account using a stolen card, the odds were just too high.
There's 9801 (99 x 99) possible outcomes that anyone trying to guess the deposits would have to pick from - vs the 99 outcomes from one payment.
In order to achieve the same number of outcomes from one payment they would have to deposit anything between 0.01 and 98.01 which would be very generous of them.
But not a UX question really.