The vmap-extractor tool skips extraction of unused maps regardless of whether --skipJunkMaps is set to true or false. I believe the error is in this line, as it checks for the presence of the -s switch, which is used for a different option:
Steps to reproduce:
Run vmap-extractor with the --skipJunkMaps false command line switch
According to the output, map 13, map 25, map 29, map 35, map 37, map 42, map 44, map 169 and map 451 are skipped
I'll create a patch shortly.