I believe the main game installer has now been updated. Redownload from the link you were provided on purchase to install the latest version from fresh without using the in-game patcher.
I am still following up with the antivirus vendor to get the updater whitelisted. Progress:
thank you, I appreciate the quickness with which you are solving the problem 
Ah well, you should leave Norton to give to anyone who uses it - as an incentive to find a halfway-decent AV.
Totally agreed on the uselessness of most antivirus programs. FWIW, I recommend a combination of malwarebytes and Microsoft security essentials. MSE is FREE and actually incredibly good. There are a very very few cases where I’ve seen malwarebytes spot something and MSE not spot it. Between them they are pretty impregnable.
Pretty much any product that you get a ‘free trial’ of preinstalled is RUBBISH. So bad, they have to pay the PC manufacturer to include it. Norton is basically malware, and should be expunged with the fire of a thousand fires. Nuke it from orbit, kill it with fire etc.
Or you could do like us oldtimers - Stop downloading porn and weird free software.
I haven’t had live AV running for … almost a decade now. I run weekly scans and I haven’t found anything in years - I haven’t ever been hit by any of the serious ones either.
You might say I use… Common Sense 1.0 
This.
My girlfriend’s PC was pretty cheap so it came installed with loads of trial stuff that you don’t need. One of them was Norton. It used the sort of language normally reserved for those scare-mongering ads you see on some sites “WARNING: Your computer may be infected. Download our software for a free scan”.
When the trial ended the program literally took over the computer bringing up an unignorable dialog saying “Leave your computer unprotected?” With a big green button to subscribe and a little red one to ignore it.
I uninstalled norton and guess what? Windows Security Essentially automatically reenabled itself. It was on the computer anyway. The computer was completely safe as long as you uninstalled Norton.
I agree with Cliff, Norton is the real malware. Is it surprising that I can’t find a valid support email to get the updater whitelisted?
OK, rant over.
Sure, I’ve not had anything too major in the last decade or so either, it never hurts to be cautious though.
Thansk for thinking about us linux users. I managed to get it working with Wine 1.7 (Ubuntu has 1.6 in the repos) just fine, so no Problems left. But yes, Wine emulates the entire Windows tree with all it’s folders. (Users/App Data)
So Updates work fine with Linux now as well
I had a slightly different issue. I downloaded the update and then it closed the game to go to the installer, like usual, but the update never installed. I probably gave it at least 5-10 minutes and it never changed from 0% installed. I don’t know the cause.
Have you tried repatching? You may have to uninstall and reinstall the game. I’m sorry for the inconvenience.
Reinstalling it seemed to work. I have also managed to keep all my saves too, so great!
[Solved]
Latest update installed for me, no problem, with MSE and Ad-aware turned on 
I have just received confirmation that Symantec (the guys who make Norton) have added Big Pharma to their whitelist. Hopefully from now on there should be no more trouble from any of their products.
If you still encounter an issue with any Norton Antivirus product then please make sure your Norton product is fully up to date. Then if you continue to have any issue let me know and I will chase Symantec.
There is a chance that Bit Defender have also whitelisted the updater but they have not confirmed with me yet. Please let me know if anyone still has issues with Bit Defender and I will chase them.
As far as I am aware that is all the Antivirus programs that were complaining covered. 
My issue seems a little bit different than the ones described here. It downloads the file just fine, and then says they are installed and the game must restart. It does that, but instead of restarting, it opens a little box called “Updater” and then the code just collapses and it stops responding and crashes. I have been unable to fix this problem and it completely disables my ability to play the updated game. I have a Windows 7 computer with no external antivirus programs.
I’m sorry you’re having trouble getting your game up to date and for any inconvenience caused. As a backup you can always redownload the game from the original link you were sent when you purchased it. We will always keep that link up-to-date in case of issues such as this. Your save progress will be preserved.
If this is not satisfactory, please tell me if there is an error log here and I will try to help with the update problem:
C:\Users<username>\AppData\Local\Temp\Crafty
Tim
Yeah, that’s what I did, and it worked. Thank you! Great job solving these problems so quickly, and It’s great that you are keeping the game up to date successfully.