I suspect you've hit a bug (your various attempts look fine to me).  The barcodes are included as pixel images, and AFAICT, Javascript is not involved here. The strange thing is that although all three tools do in fact copy the images into the merged output file, and there's also some code which is supposed to render them, this doesn't seem to happen...

At the moment I don't have the time to look into this in more detail, but if you don't mind installing yet another PDF tool (not Perl though), I'd suggest using pdftk:

pdftk label1.pdf label3.pdf cat output all.pdf
[download]

would concatenate label1.pdf and label3.pdf into all.pdf (and all barcode labels did show up fine when I tried it). You may of course also specify more than two input files.

Try to get one of the precompiled binaries... Depending on platform, pdftk can sometimes be quite a PITA to build. It depends on GCJ, which means you'll also need to have libgcj.so installed (Java runtime library for use with the gcj front end to gcc).  It's worth the trouble, though. Once you have it working, it allows you to do all kinds of manipulating PDF files. I particularly like its feature to be able to uncompress and re-compress the stream objects in the PDF files, which essentially means that you can edit the contents with your favorite text editor (or Perl :) — or debug problems like these... (You still have to know what you're doing (i.e. PDF syntax), but the tedious work like updating the xref table etc. is being done for you.)