You should put each sequence in a different folder. If the new render is additional frames for the same scene the same thing holds true. Put each render in it's own folder.
If you're adding to an existing sequence with the same file name then AE is not going to like having additional frames loading in while it's working. It would be the same thing as recapturing footage with the same file name in the same folder while you're trying to pull up the footage in another app. Rendering additional frames for the same sequence in the same folder while AE is working has always been a bad idea. You may have gotten away with it in CS5.5 but that was a fluke. It is essentially the same thing as trying to work on video while it is being captured.
If you're rendering different passes (diffuse, specular, etc.) you can get away with these additional sequences with a different file name being stored in the same folder but IMHO, this is not good project management.
Sorry, but your post is both confusing and it lacks crucial information.
For example, we don't know what you mean when you write "folder". Is the folder in AE or on the computer? That's confusing.
To help us help you, I recommend going here:
It's a good compilation of the information necessary to make an accurate diagnosis.
Sorry I was rushing when I posted this, but thank you for the info. I'll make sure to use this in future discussions.