No, unfortunately prebuffering when the song is loaded instead of when you hit play caused out of sync playback when switching to other apps and back. Therefore prebuffering is now done immediately when you press play.
But I saw in your logs that once the initial prebuffering is done, a second prebuffering when changing the playback position only took about 40ms. So maybe the solution could be to prebuffer when the song is loaded and then prebuffer a second time when playback starts. I need to investigate into this idea.
Right now, you could indeed try a different format for those two songs. Maybe 256kbit mp3 or m4a which is the native Apple format and might be a bit faster to prebuffer.
It also seems that ST3 keeps running in the background. Maybe try to quit the app in the task switcher. And also quit other apps that might need lot of processing time.