I have Windows Vista and experienced the same problem with enchanting. So I googled in search of a solution, but I didn't find anything. However I noticed that it wasn't a problem specific to the GOG version (in a forum a user with the steam version complained about this bug) and that everyone who experienced the bug had Windows Vista. Then, I found a .txt file in the Arx directory named "ARX FAQ". I read it and a question was:
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Question 1:
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How can I stop Arx Fatalis crashing all the time?
Answer:
Download the latest patch from the official site at
http://www.arxfatalis-online.com This should improve the game's stability.
If you still experience problems please ensure that you have no anti-virus software or background applications running whilst playing the game.
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So I closed every background application and lanched the game. I used a Rock of Amikar with a random short sword, cast the enchant spell and... [drums rumble] it crashed!
However, I was far from giving up and I started thinking. The game has this bug under Windows Vista. And if I try to play under a compatibility mode? I know, it looks too easy, but I tried. I set the game to run under Windows Xp SP 2 compatibility mode but it crashed as always.
I decided to try a last thing: to run the game under Windows 98 / Windows Me compatibility mode.
I used again a Rock of Amikar with a random short sword, cast the enchant spell and... [another drums rumble] it didn't crash!
The game continued to run and in my inventory I had an unbreakable short sword.
I repeated the enchanting process about five times and didn't have a single crash.
Then, I rebooted my pc and tried again. This time all the background applications that usually run on my pc were running. I tried several enchantings and all succeeded, but I had two random crashes when I was just walking around, so it's probably useful to close all unneeded backgroung applications that are running.
In conclusion, set the game to run under Windows 98 / Windows Me compatibility mode and it won't crash when you enchant something and close all the useless running background applications before playing in order to experience less random crashes (but probably you'll still have one sometimes).
I hope this can be of some help.
EDIT: It seems that if the game runs under Windows 98 / Windows Me compatibility mode you won't be able to play using your screen higher resolutions. Widescreen resolutions can be selected though.