I got it working correctly. I've posted it over at Cryptoknight's site
http://hl4e.cryptoknight.org/index.php?topic=262.0, but I'm also attaching it here. If I end up doing something in the case of Optional and expensive literacy, I'll probably just post the fix over there.
For completeness I've also included the Mark of Scribing fix. Good news is that they both stack properly, if for some reason you need 7 extra languages and two feats to burn. I didn't fix the rest of Mark of Scribing, just the languages part. That will definitely be fixed over at Crypto's site, probably next week.