Do you ever have people paying one lot of postage for multiple items? If you do, that can explain it.
eBay - for some unknown reason - divide the postage charge by the number of items in the order, then calculate the FVF on that fraction of the postage cost, then add them back up together to get the FVF on postage.
For example, lets say your postage is $5 - someone buys one item with $5 P&H, eBay calculates 10.9% of $5, and charges you 55c (rounded up from 54.5c).
Now lets say someone buys 30 items and you still only charge $5 in postage. eBay divides $5 by 30, which is 16.6 cents recurring, so they round it up to 17c. Then they charge 10.9% on 17c, 30 individual times - 10.9% of 17c is 1.85c which gets rounded up to 2c, 2c x 30 is 60c, and boom, eBay just made a cool 5c for no reason.
This happens to me multiple times a week, but the amount is too small for me to feel inclined to talk to someone at eBay about it.
Although, another site I sell on recently had to refund a lot of money to sellers because while you could list there in any currency, they would convert all amounts to USD, calculate their FVF on the converted amount, and then convert the fee back into the seller's currency, resulting in a lot of 1, 2 or 3c discrepancies. When they refunded me, the amount was around $75 from maybe a year's worth of transactions.
I wonder what eBay's tally would be if they had to do the same. 
Some round up and some round down. (You are not considering the decreases which you don't see)
The rule is .5 and up, rounded up. Anything under, rounded down.
It wouldn't surprise me if the rounding is close to even makng it eBay's legitimate funds.
I can't explain that one.
Sometimes when I make a one-off payment, paying exactly what they say I owe at the time of the payment, and check my account balance afterwards there's a -1c or +1c balance. I have no idea what causes it, though - possibly some software issue since they're dealing with fractions and percentages. It could be an Office Space kind of thing - some disgruntled office worker somewhere has worked in a bug to skim micro amounts from transactions. (I jest, but you never know... ).
