Dreamweaver CS6 - Losing Line Breaks of PHP Files

Hi all,
If this has been asked and answered, I apologize. I have scoured the forums and Google for this, but coming up empty.
Yesterday, upgraded from DW CS5 to 6. First site working on, opened up both .htm and .php files. Made simple changes, and uploaded to the server (both within, and outside of DW).
All the PHP files are immediately broken. When viewing the page code via my FTP program, all the formatting has been removed (basically line breaks). Obvioulsy, this would see like a "file type" issue. I have tried what seems to be every combination of settings in the Pref>New Document> config box and none make a difference.
I also know this could be depended on my server type (Linux). The HTML pages don't seem to mind that all the line breaks are gone from the code, but PHP pages do.
Attaching what the code looks in DW, but then looks like after I save it and view it via my FTP.
Any help would be greatly appreciated!

Hi Jon - I'm back! So - now that I have the Code Format toggled to Linux, it works perfectly when I put up my PHP files.
However, I'm learning that when I put up .html files - they go up completely empty. Everything is stripped out - when I view it within my FTP software the pages are entirely blank.
I have many sites that have files of each type, and this was never an issue with Dreamweaver 5.
Thoughts?

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