Maybe sv_pure wasn't set right? I guess you aren't already in a map when executing those commands (being in a.map already would stop sv_pure from being changed as it is cheat protected)
Try doing it from the command-line with the arguments:
I guess it should work w/o packing into pk3 (which is just a zip-archive with normal compression). Just drop your textures/folders into "Quake3/baseq3/textures".