The HTML Editor seems to change foreign charchters when the file is saved. Example, ý (Lowercase y-hachek) becomes ý. š (Lowercase s-hachek) becomes Å¡.
While the HTML itself does not look wrong in the coffeecup Editor, it is wrong in the browser and in other editors now. Is there a setting I can change to prevent the Coffeecup editor from changing the charachter?

Have you tried substituting the special characters using those available in the Editor?

I used the codes for some of the characters, but those other ones work just fine EVERY where else... until i open it in the CC Editor.

If you have special characters you need to use the special character code for all of them, not just for some. Give that a shot and see if that fixes the issue. Do keep in mind that the HTML Editor is only following protocol for what HTML tells it to do and if you don't follow it, then it can't display it correctly. Find the codes for the characters you are trying to display and see if that fixes the issue.