The same version of mkvmerge was used for the repackaging and well as packaging files that I encode with x264. Because the common item in the test was the mkvmerge program, with the same options, that leaves the video itself as the reason. The mkv file that was produced by another used a different h.264 encoder, but was wrapped by mkvmerge.
I do not have any MPEG-2 files wrapped within MKV. I do not encode MPEG-2 for archiving, wrapped with MKV. Any, and all, MPEG-2 files that I have are TS files. I suppose I could do a test MPEG-2 encode and wrap it with MKV, but I'm not sure what it will prove, since the encoder is different. Still, might be worth a try.
I could also try letting VRD encode a short piece of video to H.264 and manually wrap it with mkvmerge and see what happens. Same goes for MPEG-2, depending on the results of the H.264 test.