Just a thought, and it may not be a solution to your problem, but can you try re-uploading all files, making sure you set the transfer mode to "Auto".
FTP programs can be set upload all files in "binary" mode (for images), Ascii mode (text files) or Auto, which selects the mode based on a list of file extensions pre-defined by the user.
JPEG, JPG, GIF, FLV, MOV, WMV are examples of binary files.
HTML, CSS, JS, ASP, PHP are examples of text files (in that you can open them in any text editor and make sense of what's written).
Defining the file extension types should be able to be done through the FTP program's options menu. It depends on which one you're using, but most FTP progs have the same sort of functions and options, and this would be one of the common functions.
For example in FireFTP (from makers of firefox - this is a plugin for FF browser), under the Tools > Options then choose Uploads/DOwnloads.
There you can define the 'default' as Automatic, Binary or Ascii. This is the first thing to check as I mentioned above.
In FireFTP, you can define the 'ascii' file types. Anything else would be treated as binary.
I expect your FTP program will have similar options