TeXworks ⇒ Dependence of Encoding and Operating System

[AliceWonder]

I use TeX Live 2012 installed in CentOS 6. But I use laptop running Windows 7 with Notepad++ to edit, then transmit the sources via SCP to Linux. But going out of town, so I installed proTeXt which has TeXworks.

The files that compile perfectly in TeXLive pdflatex did not in TeXworks.

First it was complaining about missing begin of the document - I removed a commented out line above the complaint, and then further down, it complained where I include a graphic.

I commented out inclusion of the graphic. Now it runs pdflatex w/o error but some pages have these odd characters ï˙z£ at the bottom.

Is there a problem using *nix line break and UTF8 with TeXworks from proTeXt ??
What do I need to do?

Not critical, I can live with the bug until I get back from thanksgiving and can use TeX Live again, but is there something I need to do to make sure my TeX is portable between the platforms?

[AliceWonder]

It appears this isn't anything to do with TeXWorks. Changing EOL (end of line) to Windows and encoding to ANSI did solve the problem, not sure both were necessary.