Mmmmmm..... you'll notice that only 13 people have written negative comments about the program, and only four or five had problems with their writer after uninstalling. I'm not really sure. I'd say go ahead and use it and you probably won't have any problems. Some of the comments of those five where a bit fishy and indicated something other than Clonecd. It could be that a certain version had such a bug or even that it's still present, but even in the latter case you're the first that has mentioned this on this board so very few people actually have problems. I'm using a fully registered version now, but in the past I've let evaluation lapse for different versions and I never had a problem. This program is way too good to skip it just because a few people had problems with it. I advise you to go ahead and test it out. In the unlikely event that something does go wrong, come back and we'll try to solve it.
On another note, there are ways that I can get the same weird behaviour with my writer in for example Nero. When I've just burnt a cd, I have to close the progress dialog box or any cd that I insert in the writer will seem to be unreadable. I just made a habit of closing the dialog when the burn was done before testing it out.
In recap, five people with the same problem indicates that there might be a real problem, but it also suggests that by far most people never encounter it. I can assure you that maybe 10x more people let the evaluation lapse than there are who register before the time's up. If the problem really was abundant, all those people would have screamed far and wide about it. They didn't, so you're pretty safe. It's still up to you but if you want more reassurances, maybe post a question on the official
clonecd board, if there ever was a real problem like this they should be able to tell you.