Yes, it seems like they are telling you that you've lost it. That really sucks.
Are you sure it has not been credited to your account?
This is not Bitstamp's fault, it's coinexchange.io's fault. coinexchange.io has received the funds, just in a different way from what they are used to. Internal transactions are a unique feature of Ethereum. coinexchange.io knows very well that internal transactions can happen, or at least, they should know if they're working with Ethereum.
In my opinion, they should accept them. Internal transactions are not uncommon or unusual at all.
If I were you, I would send a sternly worded email or support ticket to coinexchange.io, telling them how much money it is, and requesting them to credit it to your account or return it to an address you provide. If they don't reply or tell you they can't do anything, I would escalate and send a certified letter with return receipt requested, and an email confirming the fact that you sent the letter, and the contents of the letter.
Maybe you should threaten legal action, although I don't know how much of a case you have.
If they don't cooperate, you should start complaining publicly on popular Ethereum and cryptocurrency forums, and maybe on Twitter. Try to spread some negative PR about them.
It is unacceptable that funds could be declared 'lost' in this manner, even though they have access to those same funds!
There is no technical reason why coinexchange.io can't credit it to your account and continue running their system as they normally would!