The file you linked to seems to work fine. I replaced the installbuilder.sh from the working bundle into the non-working bundle, and the non-working bundle worked.
I did a diff between the two files. Seems the only difference is that the line endings in the non-working one are "Windows" (CRLF) and working one has Unix (LF) endings.
This seems to still be cropping up. Someone else in my AI War group was playing on his Mac during our weekly game and having major issues trying to get the updates to install, and it turned out to be because of this again, in the Steam version of the game. Of course, he didn't find that out until a few days later and had to boot into Windows to play with us that night.
I also tried updating to the latest version on my MacBook today, because I borked a hard drive in my desktop and don't want to run with a degraded RAID. That's pretty much the only time I ever play on my laptop, so I was still way back at 5.000, because I had only updated to whatever Steam had auto-patched for me. The updater failed to work until I manually fixed the line endings in the script.