This page can help you compare the results of the transmuxing performed by mux.js with a known, working file produced by another tool. You could use ffmpeg to transform an MPEG-2 transport stream into an FLV with a command like this:
ffmpeg -i input.ts -acodec copy -vcodec copy output.flv
This page only compares FLVs files. There is a similar utility for testing the mp4 conversion.
Inputs
Comparison
A diff of the structure of the two FLVs will appear here
once you've specified an input TS file and a known working
FLV.