x264 skips frames in beginning after being decodec by AutoMKV

I have 13GB.mkv and i used AutoMKV to crop it down do 8GB but still maintaining the 1080p ratio. (I used Constant Quality CQ Optimized prrofile) After the that the movie skips some frames about 2 minutes in the beginning of the movie. After that, it plays well. Can someone tell me exacly what kind of settings should one use in AutoMKV to make 13GB movie smaller to 8GB without any problems.

Where did you get the 13GB movie?

From my own Blu-Ray disc

Which disc is that?

There are BDs where the main movie is very small (for video part only, Eden Lake is 12.7GiB, Saw5 is 13.9GiB...). Could be that the movie is short and/or has lots of extras and/or they didn't care to raise the bitrate to fill the disc. Remove the uncompressed and/or lossless audios, and remux it in a container with less overhead, and you have a much smaller file.