I’m not a video encoding expert so I can’t really describe in any detail as to what reference frames are. But they’re used by the codec (H.264 in this case) during the encoding/decoding process to help define upcoming frames based on compressed reference frames. The number of reference frames affects the quality of the video.
I’ve had a look at my library (the 1080p ports of which consists Blu-ray rips created by MakeMKV) and they have 3-4 reference frames. Looking at some of the default profiles for Handbrake (a cross-platform encoding application), it appears that reference frames of 1, 2, 5, and 5 are used for the very fast, fast, high quality, and super high quality profiles, respectively. So, I suspect 4-5 are plenty for a high-quality 1080p video.
Having said all that, you could try re-encoding one of the problematic files using Handbrake. If you’re not familiar with it, it’s fairly straight-forward to use. I’m not sure how nice the results will look given that these files have been encoded already however.
