I see this with PERFORCE as well ... except for me, I have set the P4 client to "UNIX" line endings, so there should never be a case where the file has CRLF.
LineEnd: unix
I just checked, the local file only has LF.
But, the file that VS copies from the version control system has CRLF throughout.
I just tried "p4 print //depot/branch/....../file.c" > blat
I found that "blat" has LF only line ending.
VS appears to be doing something to change the file to CRLF.
Another issue: In "Diff file with most up to date": [size=78%]Right-clicking on the RHS file and picking "edit file (will close this dialog)" doesn't do anything.[/size]