Upon further review it seems people have had this issue for some time.
Poppycock. No one who knows what they're doing has any trouble playing ALAC files with iTunes going back to, oh, say 2001. Even a G3 iBook can play ALAC files perfectly.
You still haven't adequately defined your issue and you're a newbie, so link to whatever Google results you're getting that you think supports your issue. Of course Applecare wouldn't know what you're talking about--you don't really know what you're talking about.
Go back to square one--this ALAC file that supposedly skips...does it skip in exactly the same place all the time, i.e. is it repeatable? If it skips in the same place every time it's a bad disc and bad rip. Try playing it back with VLC, does it skip in the same place or not?
This is connected to your AVR, try playing the suspect files back just with the Mac and headphones and NOT through the AVR--do those suspect files skip? Do they skip when played back via the ATV? If you have an iOS device or another Mac, use iTunes home sharing to play those files back on a different device--do they skip or not?
Do ALL of your ALAC files skip or is it just files from that cd? If multiple files skip, is it repeatable, i.e. do those file skip at exactly the same PLACE IN THE FILE or at various times, i.e. sporadic and random skips or dropouts?
Have you tried swapping a different cable in between your Mac and AVR?
And this is not even getting into where your iTunes media resides, your boot disk, your OS, et al.
Your superdrive is probably fine, but what is it and how is it connected to your Mac?