Well, that is certainly wrong!
How do you have your bundle defined in the admin area? What does it show the bundles price should be?
I am getting the correct price although I think the way is is displayed is very confusing.
Bob
ok i just found out that there is something wrong here.
catalog discount:
item original price: $460
our price with discount is (73%) :$124.20 usd (which calculated fine at the product page.)
now at the admin side, buy together addon /
adding a product to go with the item is fine. we select the by percentage of the original price and value of 80. which should be 460 x 80% - = $92 just like the catalogue discount.
But NOOO!!! it brings up $99.36 
if change it to "by fixed amount " then it calculates $124.20 - $80 = $44.20
“to fixed amount” (which i should want):it looks fine because it calculates or puts the number i put in the value box.
so there is something wrong in this side i guess.
ok lets say all fine at the admin side, but why would it show the same numbers i see on the admin side and at the front end but it changes after clicking add to all button?
ok i think its because we already have a discount on the items so it somewhere calculates wrong.
because on the items that doesnt have a discount it calculates correctly.
try yourselves. give your catalog a discount from the promotion. lets say in the whole store you have 50% discount (it reflects to all your products)
so now, if you want to give an extra discount (using buy together addon) to your customer if he/she buys the matching item then it calculates wrong.
because it calculates from the already discounted price i think.