As I understand it, when you use the ~nodup function, it removes duplicates at random. That is, it doesn't necessarily select the ones to remove based on type or date or anything else. It just removes all but one of the matches, randomly. Which probably is not what you want!
Instead, you probably want to sort the duplicates and figure out why you have them. Maybe you have two copies of the exact same album because your library has imported a backup copy from another disk location. I would normally say that maybe you have two different formats also, but you are using file size, so that should guarantee that you are looking at two files that are the same format.
Try this as a test. Use this expression:
[Media Type]=[audio] ~dup=[File Size],[Name] ~sort=[Artist],[Name],[Filename]
Pay attention to the file names. See if you have duplicates that are all in the same directory hierarchy, or if there is some other obvious pattern to why you have duplicates. If you find they are all in the same directory structure, you can re-sort by just filename and then delete all of the ones that are in the directories you don't want to keep.
If you have trouble, it would be a good idea to post a screen shot or some other dump that shows 10 or 20 duplicates; make sure the file name is visible. Then we can try to guide you on how to best deal with them.
Good luck.
Brian.