Why does my iPod stutter/lag while playing some songs?

I got an iPod video 30gb model in the fall and a little bit into having it, before upgrading anything, I noticed that during playback some songs would begin to lag a little bit. There'd be a sudden stutter in playback and then the stuttering would continue for the rest of the song and sometimes into the next song. I figured that this was mostly an issue with the hard drive (which only had mp3s on it), and I thought that, like the answer on another similar question here suggested, it would go away when I replaced the storage.

About a month ago, I upgraded it to an iFlash Quad with 512gb worth of microSDs. When I did this and put in my files again, I had all the lossless files in my collection converted to ALAC so they could play correctly on the stock OS synced through iTunes. However, the issue of some songs lagging has persisted, especially when using the iPod through Ford Sync in my car. I thought it only really happened during longer songs but recently it's been doing it on some songs as short as 2.5 minutes. Is there any way to fix this that isnt just trying to replace the storage again?