I've been getting this error with Dreamweaver 5.5 when I upload files using its built in FTP.
Out of interest.
Have you tried transferring the files using another third party FTP package such as CuteFTP?
I narrowed this down to the Line Break Type setting in the Dreamweaver 5.5 preferences. It was set to Windows, and as my sites are Linux I changed it to Linux and it worked from there on although I did have to edit and save my PHP files prior to uploading. I did this by adding and removing a space and then saving the file.
I spent 2 days trying to figure out what was wrong! :-)
I 'think' its a Dreamweaver 5.5 issue (well, potentially on MAC anyway).