After spending a lot of time narrowing down the issues. I have found a pattern.
Issue 1.
After a recent update, titles that have DTS audio no longer play smoothly. They skip. I have verified its not a video problem by using rips that have multiple tracks. See my video example here:
Issue 2.
A similar issue seems to be widely reported in other threads, but from what I've seen no one seems to have pinpointed the issue. For some reason 25fps files using AAC audi