Dreamweaver 6 corrupts files when uploading via Dreamweaver ftp tool

When I use Dreamweaver to upload a file very often something gets corrupt. Javascript ceases to work. The page runs locally and javascript works. The file is fine when I upload with a different ftp tool (fetch, Transmit, etc).
When I view the source of the non-working file the code looks all garbled.
When I upload the file witha diftterent ftp tool, all is well.
Never saw this before. What's up?
Using Mac, Lion, latest versions.

You can see a sample page here
The js is a simple date script I've been using for years.
Check out the formatting change after the upload with CS6 - This ONLY happens with CS6.
Server - Linux,  apache 2.2.22
Local - iMac 2.8ghz core i7 OS 10.8

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