Your comments

It shouldn't have duplicate entries for the same file in the same folder. It could display duplicate entries if you have two files with the same name in different folders.

Yes, currently you cannot easily use FTP with external files, but I haven't found a good solution for this problem yet.
Currently Textastic does never write a BOM when saving UTF-8 files, so if it exists it is removed when you change the file contents.

I'll consider changing this behavior.
Does it work again if you do a single tap once on the editor area? This should make it regain the keyboard focus.
If you have a file open in Safari, you can tap on the address bar and replace http:// with textastic:// and hit return. Textastic will open and it will download the file over http.

This is document at the bottom of this document: http://www.textasticapp.com/v4/manual/x-callback-url.html

You can also use the bookmarklet from http://feedback.textasticapp.com/topic/204856-bookmarklet-for-safari-and-textastic/
Currently Textastic supports codepage 855 "Cyrillic (DOS)" if you do a long press on the file name and choose "Open with Encoding". I'll add codepage 866 "Russian (DOS)". Thanks!