I can't create a torrent from a folder that has a tilde in it. It doesn't have a problem with tilde's in filenames, but it doesn't recognize folders with them.

I have found that Tixati will download torrents that include folders with tilde's in them, but if a tilde is the last character in the folder name it will change it to an underscore.

I have the same problem.
Trailing tilde in downloaded files is replaced by underscore. Right now I had one torrent with broken functionality because of that

This issue has not been solved in 2.12

thats because there is no issue. tilde cant be used to remain cross-platform compatible.

If a program _forcibly_ and _silently_ renames your files (and this "feature" isn't documented properly) then that's an issue.
A simple #ifdef check in code would make it cross-compatible between different platforms while keeping hidden file issue in linux solved.

It is documented that is why so many know it. Might I be so bold as to suggest you read the documentation? There are many ways to skin a cat, this cat is skinned this way, live with it and choose a different character.

Would you kindly point me to the documentation page which mention this?
I've browsed through few possibly relevant topics on http://support.tixati.com/  and didn't find anything related to auto-renaming