It seems that the cd is working, and I noticed $err is printing out "Can't open perl script "getEnvs.pl": No such file or directory." which is weird, because I know for a fact that it is there. I can manually create an ssh session, and copy and paste those same commands from my script to my ssh, and they work fine. I tried being more specific with the cd path, but that didn't seem to make a difference either.