If it's a brand new hard drive then I doubt a bad sector would cause such problems and you can normally tell when it is a bad sector as it will struggle to read the file rather than just crash out of explorer. If the old hard disk had a bad sector then it would cause problems whilst copying and it sounds like it did not do this. I know windows does have limits in the number of folders in a tree as well as files in folders so it might be something along these lines because if it words higher up the tree, then it can't be the files. How many files & folders do you have?
The link below gives some facts about the size limitations:
http://www.microsoft.com/resources/d...c_fil_tdrn.asp