You might get quicker and more accurate responses by posting these in the X5 thread, but to start, how did you transfer the files into the X5? Did you just drag and drop in Explorer? Also, those files purchased from iTunes - are they also ALAC? I haven't really encountered any ALAC in there last I checked, usually just 320kbps, but ever since I couldn't find the music I want in ALAC I never checked the iTunes music store again.
The problem with using a non-iTunes program to rip your CDs is that you should never, ever, ever, have iTunes and another music player in the same computer because iTunes is the psychotic, overly attached girlfriend among music players - you might as well invite your mistress to live in the same house as your wife. If you've already sold your Classic and will also use something like MediaMonkey to rip and play music on your computer it's good, but if you still have any Apple devices that will need iTunes, it might cause a lot of conflicts with the other player, although you might still want to try as long as you will only use the other ripper for ripping music and never for playing them on the computer, and if you use FLAC for the X5 just transfer them to an external drive straight away.
I used to have iTunes on my work/light gaming laptop to sync my iPad, both for music as well as PDF files of academic journals that I use for lectures and research, but after I updated to Tunes11 (and when you update iOS sometimes you can't use iTunes until you also get the latest version), it went back to what it was doing in previous versions (pre-iOS9 and 10) and started hogging all the audio files. It can't play FLAC, but even while playing through MM and iTunes isn't running, the tracks on its library will grey out and I can't play them anymore. Uninstalled iTunes and it worked properly again; reinstalled and again made sure iTunes is set to associate with only one (empty) iTunes folder, and two minutes later the same getting hacked in a Hollywood movie thing with files disappearing in real time started happening again. I ended up uninstalling iTunes and using my desktop gaming rig to sync the iPad, which works fine except I've always imagined this thing will only be for gaming, with no horde of tiny files clogging the lone 1.5TB platter drive in it.