You shouldn't be charged any internal fees at all 
for the bid as you describe it.

The only time you would be charged internal fees 
is if the maximum bid on the auction itself (as 
seen on the Yahoo Japan's item details page) did 
NOT go high enough to outbid ACbidder2.

For example:

ACbidder2 bids 28,000yen
You bid 45,000yen
Japan-boy1 only bids 10,000yen.

In that case, the final bid on the auction would 
show as 10,500yen (according to Yahoo Japan) with 
AnimeChaos as the top bidder. You win because 
your bid was the highest of the two AnimeChaos 
bids, but you would need to pay internal bidding 
fees for the amount between 10,500yen (the final 
cost of the auction) and 28,000yen (ACbidder2's 
maximum bid).

Hope that clears it up! ^_^

Many Sharp Smiles,
--Drac