Your comments

I had looked at that, however I have an iPhone 6, and Chunky apparently isn't available for the iPhone. On the developer's site he states that he didn't care for developing for it.
Sad thing is, I can't code myself out of a wet paper bag, otherwise I would try and write one.
I agree that for now I would like to see more core features added to Ubooquity than for it to scan each file for a malformed comic. I'm the one who sent Tom the broke files and he deduced that it was the ridiculous garbage files that OS X adds to the files. I still use my Mac to compile my books, I just do it from the command line now since it doesn't add the hidden files that way.
Yep, that's what fixed it! Thanks!

In case anyone else runs into this, I just ran this on the books on my server: zip --delete "__MACOSX/*" <name of comicbook>.cbz, then rescanned.
just emailed a link to you. Thanks!