ffmpeg concat with or without audio
Use the concat demuxer instead:

Create a text file of the following format

file 'C:\source.mp4'
inpoint 0
duration 1
file 'C:\source.mp4'
inpoint 3
duration 1
file 'C:\source.mp4'
inpoint 6
duration 1
file 'C:\source.mp4'
inpoint 9
duration 1


Then run

ffmpeg -f concat -i file.txt -map 0:v -map 0:a? -vcodec h264 -acodec aac -pix_fmt yuv420p -strict -2 -fflags +genpts C:\output.mp4