By the way, seeing as how these rips are roughly 35-36GB each (which is fine on my HTPC), I wanted to encode them to smaller files for transfer to my other computer. I tried Handbrake, but must have really screwed up something, because the resulting video lagged/stuttered all the way through. Sound was screwed up too (I chose the DTS track and chose DTS "through" or whatever it's called, and no subtitle tracks ever appeared in Handbrake). Wanted to crop the black bars out too, while keeping the same exact aspect ratio/horizontal resolution - guess choosing "Strict" was the wrong choice?
HandBrake doesn't support Blu-ray PGS subtitles.
You will have to merge the subtitles from MakeMKV's output with HandBrake's output.
HandBrake 0.9.5 cannot handle DTS-HD in MKV (this is the most likely cause of your audio issue).
Since you apparently used "DTS Passthru", it's the most likely cause of the stutter issue as well.
The nightly builds can handle it (you can re-encode the DTS core or pass the whole track through).
Anamorphic Strict is completely unrelated to your issues (stuttering or otherwise); it just ensures
that the source's dimensions are strictly
preserved (no scaling). Anamorphic Loose, on the other
hand, will adjust the width/height so that they divide evenly by 16 (but preserves the display aspect
ratio by adjusting the pixel aspect ratio).