Have just had the chance to test this update, and noticed something that didn't happen when I tested the first, limited, test of the auto-updater.
I uninstalled that version, installed from latest client (as given by the getURL page), unclicked the run checkbox at the end of the installer, and then installed this update.
When Frozen Synapse then ran, at the end of the update, my Norton Internet Security 2011 Netbook Edition (AKA NIS) started to run a SONAR Scan on update_fs.exe - Frozen Synapse then continued to load ok, but I quit so that I could restore my backed-up Single Player Campaign files, recorded videos, and preferences.
Now, when I re-ran Frozen Synapse, NIS was still doing the SONAR Scan, and Frozen Synapse displayed a message saying the update had failed and then it (FS) crashed.
NIS then finished scanning update_fs.exe and told me it had removed the file to quarantine!
So, I told NIS to restore and trust it.
Frozen Synapse now appears to work ok (I've just re-ran it, and it is, as I type this, sitting in the background on the log-in screen).
So, for future reference, any users of NIS should probably, after installing the update, not auto-run FS, and instead find update_fs.exe and tell NIS to trust it.
Posting with the intention of provoking a reaction.