FFMPEG Converting MKV to MP4 causes Frame Rate Mode to Change

When I convert a video from MKV to MP4 using this command:

ffmpeg -i input.mkv -vcodec copy -acodec copy output.mp4

the frame rate mode changes from Constant to Variable, creating a desync over time in Adobe Premiere. Is there a way to keep the frame rate constant?

EDIT: Console Output from FFMPEG

F:\Recordings\Gameplay\Test>ffmpeg -i input.mkv -vcodec copy -acodec copy output.mp4
ffmpeg version N-82178-g60178e7 Copyright (c) 2000-2016 the FFmpeg developers
built with gcc 5.4.0 (GCC)
configuration: --enable-gpl --enable-version3 --disable-w32threads --enable-dxva2 --enable-libmfx --enable-nvenc --enable-avisynth --enable-bzlib --enable-libebur128 --enable-fontconfig --enable-frei0r --enable-gnutls --enable-iconv --enable-libass --enable-libbluray --enable-libbs2b --enable-libcaca --enable-libfreetype --enable-libgme --enable-libgsm --enable-libilbc --enable-libmodplug --enable-libmp3lame --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-libopenh264 --enable-libopenjpeg --enable-libopus --enable-librtmp --enable-libschroedinger --enable-libsnappy --enable-libsoxr --enable-libspeex --enable-libtheora --enable-libtwolame --enable-libvidstab --enable-libvo-amrwbenc --enable-libvorbis --enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx264 --enable-libx265 --enable-libxavs --enable-libxvid --enable-libzimg --enable-lzma --enable-decklink --enable-zlib
libavutil      55. 35.100 / 55. 35.100
libavcodec     57. 65.100 / 57. 65.100
libavformat    57. 57.100 / 57. 57.100
libavdevice    57.  2.100 / 57.  2.100
libavfilter     6. 66.100 /  6. 66.100
libswscale      4.  3.100 /  4.  3.100
libswresample   2.  4.100 /  2.  4.100
libpostproc    54.  2.100 / 54.  2.100
Input #0, matroska,webm, from 'input.mkv':
Metadata:
ENCODER         : Lavf57.41.100
Duration: 00:00:10.83, start: 0.000000, bitrate: 8834 kb/s
Stream #0:0: Video: h264 (Constrained Baseline), yuv420p(progressive), 1920x1080, SAR 1:1 DAR 16:9, 1k fps, 60 tbr, 1k tbn, 120 tbc (default)
Metadata:
  DURATION        : 00:00:10.834000000
Stream #0:1: Audio: aac (LC), 44100 Hz, stereo, fltp (default)
Metadata:
  title           : Mic
  DURATION        : 00:00:10.797000000
Stream #0:2: Audio: aac (LC), 44100 Hz, stereo, fltp (default)
Metadata:
  title           : Desktop
  DURATION        : 00:00:10.797000000
Stream #0:3: Audio: aac (LC), 44100 Hz, stereo, fltp (default)
Metadata:
  title           : Discord
  DURATION        : 00:00:10.797000000
Output #0, mp4, to 'output.mp4':
Metadata:
encoder         : Lavf57.57.100
Stream #0:0: Video: h264 (Constrained Baseline) ([33][0][0][0] / 0x0021), yuv420p(progressive), 1920x1080 [SAR 1:1 DAR 16:9], q=2-31, 1k fps, 60 tbr, 16k tbn, 1k tbc (default)
Metadata:
  DURATION        : 00:00:10.834000000
Stream #0:1: Audio: aac (LC) ([64][0][0][0] / 0x0040), 44100 Hz, stereo (default)
Metadata:
  title           : Mic
  DURATION        : 00:00:10.797000000
Stream mapping:
Stream #0:0 -> #0:0 (copy)
Stream #0:1 -> #0:1 (copy)
Press [q] to stop, [?] for help
frame=  650 fps=0.0 q=-1.0 Lsize=   11681kB time=00:00:10.81    bitrate=8846.5kbits/s speed= 347x
video:11362kB audio:302kB subtitle:0kB other streams:0kB global headers:0kB muxing overhead: 0.145660%

F:\Recordings\Gameplay\Test>pause
Press any key to continue . . .

It changes to VFR because your original material (MKV) is actually VFR, just detected wrong. It is a very common problem among multiple libraries I have been working with.

Essentially, the concept of "framerate" does not exist in MKV container, let alone CFR/VFR. Instead, every single video frame has a timecode. Most of utilities (ffmpeg, mediainfo etc.) just use the timecodes to calculate the framerate as will as frame rate mode. For obvious performance concerns, They can't/don't read the whole file, so sometimes the info is off. You can use mkvextract to extract the timecodes of all the frames and calculate the interval between them across the whole video, to see if it's actually fully CFR or VFR.