The fighter can only using his "attack the shifting monster" power if he knows its shifting. as a DM you are under no obligation to telling him the character is shifting, and there is no amount of perception checking that can tell him the guy is shifting. He might perception check his way into knowing that the monster is no longer next to him, or maybe even discern his final square, but he can't tell if he's shifting, moving one square, teleporting one sqaure, flying one square, bunny-hopping one square or just getting so fat he takes up two squares, but then shrinks down to one square again but in the new square instead. The DM is under no obligation to tell the player what the invisible man is doing, just the end percieved results of what square he's in (possibly which squares he moved through). If you can't even get an OA off when you may well have noticed something run by you, you'll not 'see' any difference when it shifts, and you won't be able to take any usually triggered actions.
Bottom line: the most you know about something you can't see is what square its in, that is it. You can't trigger on something you can't see, and you need to see shifting to KNOW its happening.