The way I understand it
When the game hosts, it checks all the CD keys to make sure they are good.
And then it checks the turned in turn files against each other (but skips the host key).
If it can see that two computers are using the same key, then it considers it a cheat.
No matter what good reasons and logic you have (like both being your computers) it has no way of telling that from an illegal copy. So basically, avoid having 2 computers using the same key in the same game, (on the same turn?) to avoid that particular part of the security check.
For hosts:
there is a --verify switch that will provide a way to check all the turn in files before hosting to help avoid messy rollbacks in case someone is taking an action you are unsure of.