Windows replaces language specific characters (I’m helpless)

Good people of internet. I welcome you here and i want to present you with the reason you all came here for: Muffin Knight giveaway

And now let’s get down to business with those, who actually want to help!
I just freshly reinstalled windows 7 with english language as default. I’ve set everything else to my language specific (slovak, in my case), including date formats, location and keyboard input. I also downloaded slovak language pack but i don’t use it.
When trying to use subtitles, i found out that some of my language specific characters don’t work. For example, characters like č,š,ž,é and so on are replaced ø,è,ì and so on.
At first i thought, this was just a problem with subtitles, but those characters were replaced in the file as soon as i downloaded it. So i installed PSPad and found out, that even in instalation wizard, those characters are replaced. That means this problem is windows-wide. However it does not affect my browser or even Windows language itself when i set it to slovak.
What i found out next, was that when i opened those subtitles with PSPad, it was automatically corrected. No strange characters. Someone told me, that it has something to do with "encoding" so looked at it and PSPad encoding was set to CP1250. But when i saved that document with PSPad and opened it with different text editor, it was back to previous - fucked up - state.
Please can someone help me, because "googling" is huge pain in the ass and i haven’t found any windows-wide solution.