Hi Disruptive,
This sounds like something which we are currently changing. I would imagine that you are chaning the keywords in the Folder view. If you then click on the domain name, you'll probably see that the previous keyword is set for each ad region. So, you now have one keyword for "all regions" and separate keywords for each individual ad region, which overwrite the 'all regions' keyword. This is obviously not an ideal situation, so we are looking at simplifying the issue.
For now, you can get round it by clicking 'cascade on ad regions' when changing keywords.
Hope this helps a bit.
Ed