A few things that can make Git show the entire file as changed:
Line endings -- but you said you checked these and they're the same;
Indentation -- VS (especially if you have some extensions installed) might change the indentation from tabs to spaces or vice-versa. You can check this with "Show Whitespace" (Ctrl-R, Ctrl-W in VS or the relevant option in your differ).
Encoding -- if VS decides to re-encode the file in some different encoding (e.g. UTF16) it might show up as entirely changed although the textual representation would look the same.