Your comment about including and excluding files made me think that you were talking about A1Click scanning for problems.
After rereading your original post, it seems like you are talking about the cleaning process. If it is the cleaning process, then my guess is that you have the No Remains Deletion on. On huge files it can take hours and if your computer cannot handle it, it may freeze up. With No Remains Deletion, A1Click goes to each byte of the file and rewrites the bytes many times. This can take a very, very long time.
I suggest that you uncheck No Remains Deletion.