@Pranalipatel – I noticed that too about 6 months ago when we tested rtMedia with the free encoder. The quality issue comes down to wmv files most of the time. The bitrate of the encoding service is so low that the quality is just junk. It was also this way on the ffmpeg encoder with node. I rewrote the ffmpeg commands to this:
var command = 'ffmpeg -y -i ' + queued_folder + current_file.filename + ' -acodec libfaac -b:a 96k -s 1280x720 -vcodec libx264 -movflags faststart -profile:v baseline -pix_fmt yuv420p -level:v 30 -crf 31 -threads 4 "' + temp_folder + filename + '"';
The thumbnails ffmpeg commands did not need updating, only the actual encoding one. You might strip out the -s 1280x720 because that forces all videos to be a set resolution and aspect ratio but for me, that setting is nice.
If this helps, cool! If not, no worries, maybe it might help someone else.