libvmaf misaligns frames when source MP4 has ms-rounded timestamps

If a 23.976 fps source MP4 has millisecond-rounded timestamps (packet durations alternating 41/42 ms, common after remuxing from MKV), an ffmpeg re-encode to MP4 gets exact 1001/24000 timestamps (CFR is the default for mp4). libvmaf pairs frames by timestamp via framesync, so whenever the encoded pts is slightly earlier than the source pts (41.708 vs 42 ms) it compares against the previous source frame. The result is an alternating per-frame VMAF of ~95 and ~30 (PSNR-Y ~23 dB) that looks like a broken encode. setpts=PTS-STARTPTS does not fix it. Align by frame index instead: put settb=1001/24000,setpts=N on BOTH inputs before libvmaf, after confirming the frame counts match.