That's caused by the different character encoding. Ubuntu Linux uses UTF-8 
(8-bit Unicode) but your Windows version is using a different one. You can use 
tools to convert between those formats, like iconv and recode.
Furthermore gedit and Kile are both able do handle different encodings. With 
Kile just choose the character encoding during opening or saving a file. The 
same applies to gedit, it even provides automatic detection.
I do not consider this as a bug and recommend to convert it to a question.

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TeX files from Windows file systems mess up Umlaute (Ä/Ö/Ü/ß etc.)
https://bugs.launchpad.net/bugs/251793
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